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Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

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Journal of Integrative Agriculture 2024年第7期23卷 2178-2195页

作者： Peng Liu Langlang Ma Siyi Jian Yao He Guangsheng Yuan Fei Ge Zhong Chen Chaoying Zou Guangtang Pan Thomas Lübberstedt Yaou Shen State key laboratory of Crop Gene Exploration and Utilization in southwest China/maize research institute Sichuan Agricultural UniversityChengdu 611130China Department of Agronomy Iowa State UniversityAmesIA 50011USA

genetic transformation has been an effective technology for improving the agronomic traits of ***,it is highly reliant on the use of embryonic callus(EC)and shows a serious genotype *** this study,we performed genomic sequencing for 80 core maize germplasms and constructed a high-density genomic variation map using our newly developed pipeline(MQ2Gpipe).Based on the induction rate of EC(REC),these inbred lines were categorized into three *** low-REC germplasms displayed more abundant genetic diversity than the high-REC *** integrating a genome-wide selective signature screen and region-based association analysis,we revealed 95.23 Mb of selective regions and 43 REC-associated *** variants had phenotypic variance explained values ranging between 21.46 and 49.46%.In total,103 candidate genes were identified within the linkage disequilibrium regions of these REC-associated *** genes mainly participate in regulation of the cell cycle,regulation of cytokinesis,and other functions,among which MYB15 and EMB2745 were located within the previously reported QTL for EC *** leaf area-associated variants with large effects were closely linked to several REC-related loci,implying a potential synergistic selection of REC and leaf size during modern maize breeding.

关键词： maize genetic transformation embryonic callus selective signal association analysis

Identification of propranolol and derivatives that are chemical inhibitors of phosphatidate phosphatase as potential broad-spectrum fungicides

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Plant Communications 2024年第1期5卷 215-230页

作者： Juan Zhao Yu Chen Zhifen Ding Yaru Zhou Ruiqing Bi Ziting Qin Lei Yang Peng Sun Qiping Sun Guang Chen Daiyuan Sun Xianya Jiang Lu Zheng Xiao-Lin Chen Hu Wan Guanghui Wang Qiang Li Huailong Teng Guotian Li National key laboratory of agricultural Microbiology Hubei Hongshan LaboratoryHubei Key Laboratory of Plant PathologyThe Center of Crop NanobiotechnologyHuazhong Agricultural UniversityWuhan 430070China College of Science Huazhong Agricultural UniversityWuhan 430070China National key laboratory of Crop genetic improvement Huazhong Agricultural UniversityWuhan 430070China State key laboratory of Crop Stress biology for Arid Areas College of Plant ProtectionNorthwest A&F UniversityYangling 712100China College of Chemistry and Life Sciences Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological ResourcesChengdu Normal UniversityChengdu 611130China Yangjiang institute of agricultural Sciences Yangjiang 529500China

Plant diseases cause enormous economic losses in agriculture and threaten global food security,and application of agrochemicals is an important method of crop disease *** of disease-resis-tance mechanisms and synthesis of highly bioactive agrochemicals are thus important research ***,we show that propranolol,a phosphatidate phosphatase(Pah)inhibitor,effectively suppresses fungal growth,sporulation,sexual reproduction,and infection of diverse *** MoPah1 enzyme activity of the rice blast fungus Magnaporthe oryzae is inhibited by *** in lipid metabolism are associated with inhibited hyphal growth and appressorium formation caused by propranolol in *** inhibits a broad spectrum of 12 plant pathogens,effectively inhibiting infection of barley,wheat,maize,tomato,and *** improve antifungal capacity,we synthesized a series of propranolol derivatives,one of which shows a 16-fold increase in antifungal ability and binds directly to *** and its derivatives can also reduce the severity of rice blast and Fusarium head blight of wheat in *** together,our results demonstrate that propranolol suppresses fungal development and infection through mechanisms involved in lipid *** and its derivatives may therefore be promising candidates for fungicide development.

关键词： propranolol molecular design chemical modification virulence lipid metabolism Pyricularia oryzae

Transcriptomic responses in resistant and susceptible maize infected with Fusarium graminearum

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The Crop Journal 2020年第1期8卷 153-163页

作者： Guangsheng Yuan Xiujing He Hui Li Kui Xiang Li Liu Chaoying Zou Haijian Lin Jiali Wu Zhiming Zhang Guangtang Pan key laboratory of biology and genetic improvement of maize in southwest region of Ministry of Agriculture Maize Research InstituteSichuan Agricultural University

Gibberella ear rot(GER)caused by Fusarium graminearum(teleomorph Gibberella zeae)is a common maize disease that not only severely reduces grain yield but also contaminates maize grain with *** investigated the molecular mechanism underlying the host defense responses against pathogen infection using comparative transcriptomic *** injected *** spore suspensions into plants of resistant(IBM-81)and a susceptible(IBM-85)maize inbred line after pollination and performed RNA-seq 48,72,and 96 h after *** 487 and 410 differentially expressed genes(DEGs)were induced in the resistant and susceptible lines across three time points,indicating that a stronger defense response was activated in the resistant than in the susceptible *** them,198 genes commonly induced in the two lines were subjected to pathway analysis,revealing that most of the DEGs were closely associated with defense and a wide range of metabolic *** associated with pathogenesis-related protein 1(PR1)and regulation of salicylic acid were significantly enriched during *** infection,suggesting that these DEGs play dominant roles in maize resistance to *** results provide a resource for future gene discovery and facilitate elucidation of the complex defense mechanisms involved in resistance to GER.

关键词： Gibberella ear rot Fusarium graminearum Molecular mechanism RNA-seq Differentially expressed genes

Overexpression of the Suaeda salsa SsNHX1 gene confers enhanced salt and drought tolerance to transgenic Zea mays

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Journal of Integrative Agriculture 2018年第12期17卷 2612-2623页

作者： HUANG Ying ZHANG Xiao-xia LI Yi-hong DING Jian-zhou DU Han-mei ZHAO Zhuo ZHOU Li-na LIU Chan GAO Shi-bin CAO Mo-ju LU Yan-li ZHANG Su-zhi key laboratory of biology and genetic improvement of maize in southwest region Ministry of Agriculture/Maize Research Institute Sichuan Agricultural University

maize is one of the most important crops worldwide, but it suffers from salt stress when grown in saline-alkaline soil. There is therefore an urgent need to improve maize salt tolerance and crop yield. In this study, the SsNHX1 gene of Suaeda salsa, which encodes a vacuolar membrane Na~+/H~+ antiporter, was transformed into the maize inbred line 18-599 by Agrobacterium-mediated transformation. Transgenic maize plants overexpressing the SsNHX1 gene showed less growth retardation when treated with an increasing NaCl gradient of up to 1%, indicating enhanced salt tolerance. The improved salt tolerance of transgenic plants was also demonstrated by a significantly elevated seed germination rate(79%) and a reduction in seminal root length inhibition. Moreover, transgenic plants under salt stress exhibited less physiological damage. SsNHX1-overexpressing transgenic maize accumulated more Na~+ and K~+ than wild-type(WT) plants particularly in the leaves, resulting in a higher ratio of K~+/Na~+ in the leaves under salt stress. This result revealed that the improved salt tolerance of SsNHX1-overexpressing transgenic maize plants was likely attributed to SsNHX1-mediated localization of Na~+ to vacuoles and subsequent maintenance of the cytosolic ionic balance. In addition, SsNHX1 overexpression also improved the drought tolerance of the transgenic maize plants, as rehydrated transgenic plants were restored to normal growth while WT plants did not grow normally after dehydration treatment. Therefore, based on our engineering approach, SsNHX1 represents a promising candidate gene for improving the salt and drought tolerance of maize and other crops.

关键词： Na^+/H^+ antiporter salt stress K^+/Na^+ drought stress gene transformation

Genome-Wide Expression Profile of maize Root Response to Phosphorus Deficiency Revealed by Deep Sequencing

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Journal of Integrative Agriculture 2014年第6期13卷 1216-1229页

作者： SU Shun-zhong WU Ling LIU Dan LU Yan-li LIN Hai-jian ZHANG Shu-zhi SHEN Ya-ou LIU Hai-lan ZHANG Zhi-ming RONG Ting-zhao ZHANG Xiao TIAN Yue-hui NIE Zhi GAO Shi-bin key laboratory of biology and genetic improvement of maize in southwest region Ministry of Agriculture/Maize Research InstituteSichuan Agricultural University

Phosphorus （P） is one of the three primary macronutrients that are required in large amounts for plant growth and development. To better understand molecular mechanism of maize and identify relevant genes in response to phosphorus deficiency, we used Solexa/Illumina＇s digital gene expression （DGE） technology to investigate six genome-wide expression profiles of seedling roots of the low-P tolerant maize inbred line 178. DGE studies were conducted at 6, 24 and 72 h under both phosphorus deficient and sufficient conditions. Approximately 3.93 million raw reads for each sample were sequenced and 6 816 genes exhibited significant levels of differential expressions in at least one of three time points in response to P starvation. The number of genes with increased expression increased over time from 6 to 24 h, whereas genes with decreased expression were more abundant at 72 h, suggesting a gradual response process for P deficiency at different stages. Gene annotations illustrated that most of differentially expressed genes （DEGs） are involved in different cellular and molecular processes such as environmental adaptation and carbohydrate metabolism. The expression of some known genes identified in other plants, such as those involved in root architecture, P metabolism and transport were found to be altered at least two folds, indicating that the mechanisms of molecular and morphological adaptation to P starvation are conserved in plants. This study provides insight into the general molecular mechanisms underlying plant adaptation to low-P stress and thus may facilitate molecular breeding for improving P utilization in maize.

关键词： maize phosphorus efficiency root digital gene expression

Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

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The Crop Journal 2022年第1期10卷 47-55页

作者： Fei Ge Jingtao Qu Peng Liu Lang Pan Chaoying Zou Guangsheng Yuan Cong Yang Guangtang Pan Jianwei Huang Langlang Ma Yaou Shen key laboratory of biology and genetic improvement of maize in southwest region Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina Berry Genomics Corporation Beijing 100015China

The current assembled maize genomes cannot represent the broad genetic diversity of maize *** more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in *** we describe the genome sequence and annotation of A188,a maize inbred line with high phenotypic variation relative to other lines,acquired by single-molecule sequencing and optical genome *** assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases(Mb),compared to 9.73 Mb for B73 and 10.2 Mb for *** on the B73_Ref Gen_V4 genome,295 scaffolds(2084.35 Mb,94.30%of the final genome assembly)were anchored and oriented on ten *** analysis revealed that~30%of the predicted A188 genes showed large structural divergence from B73,Mo17,and W22 genomes,which causes high protein divergence and may lead to phenotypic variation among the four inbred *** a line with high embryonic callus(EC)induction capacity,A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in *** our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.

关键词： maize Embryonic callus A188 Genome assembly Single-molecule sequencing

Association mapping for root system architecture traits under two nitrogen conditions in germplasm enhancement of maize doubled haploid lines

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The Crop Journal 2020年第2期8卷 213-226页

作者： Langlang Ma Chunyan Qing Ursula Frei Yaou Shen Thomas Lübberstedt Department of Agronomy Iowa State UniversityAmes 50010USA key laboratory of biology and genetic improvement of maize in southwest region Maize Research InstituteSichuan Agricultural UniversityChengdu 611130China

Root system architecture(RSA)contributes to nitrogen(N)uptake and utilization in *** this study,a germplasm enhancement of maize double haploid population of 226 lines genotyped with 61,634 SNPs was used to investigate the genetic basis of RSA under two N levels using a genome-wide association study(GWAS).GLM+PCA,FarmCPU,and MLM models were utilized to balance false positives and false *** total,33 and 51 significant SNP-trait associations were detected under high and low N conditions,*** high N,SNP S9_2483543 was detected by all *** disequilibrium(LD)regions of some SNPs overlapped with the intervals of QTL for RSA and N response that were detected in previous *** particular,several known genes,Rtcs,Rtcl,Rtcl,and Ms44,were located in the LD regions of S1_9992325,S9_151726472,S9_154381179,and S4_197073985,*** the candidate genes identified by this study,GRMZM2G139811,GRMZM2G314898,GRMZM2G054050,GRMZM2G173682,GRMZM2G470914,GRMZM2G462325,GRMZM2G416184,and GRMZM2G064302 were involved in seedling,seed,and root system development or N metabolism in Arabidopsis or *** markers identified in this study can be used for marker-assisted selection of RSA traits to improve nitrogen use efficiency in maize breeding,and the candidate genes will contribute to further understanding of the genetic basis of RSA under diverse N conditions.

关键词： germplasm breeding seedling

ZmMS39 encodes a callose synthase essential for male fertility in maize(Zea mays L.)

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The Crop Journal 2023年第2期11卷 394-404页

作者： Qunkai Niu Ziwen Shi Peng Zhang Shuai Su Bin Jiang Xiaowei Liu Zhuofan Zhao Suzhi Zhang Qiang Huang Chuan Li Tao Yu Hongyang Yi Tingzhao Rong Moju Cao key laboratory of biology and genetic improvement of maize in southwest region Maize Research InstituteSichuan Agricultural UniversityChengdu 611130SichuanChina Chengdu agricultural College Chengdu 611130SichuanChina sichuan institute of Atomic Energy Chengdu 611130SichuanChina

Callose contributes to many biological processes of higher plants including pollen development,cell plate and vascular tissue formation,as well as regulating the transport function of *** functions of callose synthase genes in maize have been little *** describe a maize male-sterile mutant 39(ms39)characterized by reduced plant *** this study,we confirmed using CRISPR/Cas9 technology that a mutation in Zm00001d043909(ZmCals12),encoding a callose synthase,is responsible for the male sterility of the ms39 *** with male-fertile plants,callose deposition around the dyads and tetrads in ms39 anthers was significantly *** cell autophagy observed in ms39 anthers may have been due to the premature programmed cell death of tapetal cells,leading to collapse of the anther wall *** glucose metabolism in ms39 may have intensified autophagy in *** of the ms39 gene on maize heterosis by paired-crossed experiment with 11 maize inbred lines indicated that ms39 can be used for maize hybrid seed production.

关键词： maize Genic male sterility Callose synthase Tapetal PCD Anther and pollen development Autophagy

Repetitive sequence analysis and karyotyping reveal different genome evolution and speciation of diploid and tetraploid Tripsacum dactyloides

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The Crop Journal 2016年第4期4卷 247-255页

作者： Qilin Zhu Zexi Cai Qilin Tang Weiwei Jin National maize improvement Center of China Beijing Key Laboratory of Crop Genetic Improvement Coordinated Research Center for Crop Biology China Agricultural University maize research institute Sichuan Agricultural University

In the subtribe Maydeae, Tripsacum and Zea are closely related genera. Tripsacum is a horticultural crop widely used as pasture forage. Previous studies suggested that Tripsacum might play an important role in maize origin and evolution. However, our understanding of the genomics and the evolution of Tripsacum remains limited. In this study, two diploids,T. dactyloides var. meridionale(2n = 36, MR) and T. dactyloides(2n = 36, DD), and one tetraploid,T. dactyloides(2n = 72, DL) were sequenced by low-coverage genome sequencing followed by graph-based cluster analysis. The results showed that 63.23%, 59.20%, and 61.57% of the respective genome of MR, DD, and DL were repetitive DNA sequence. The proportions of different repetitive sequences varied greatly among the three species. Fluorescence in situ hybridization(FISH) analysis of mitotic metaphase chromosomes with satellite repeats as the probes showed that the FISH signal patterns of DL were more similar to that of DD than to that of MR. Comparative analysis of the repeats also showed that DL shared more common repeat families with DD than with MR. Phylogenetic analysis of internal transcribed spacer region sequences further supported the evolutionary relationship among the three species. Repetitive sequences comparison showed that Tripsacum shared more repeat families with Zea than with Coix and Sorghum. Our study sheds new light on the genomics of Tripsacum and differential speciation in the Poaceae family.

关键词： Tripsacum Low-coverage sequencing Repetitive sequence Karyotype Phylogenetic analysis