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Shen X, Xiao B, Kaderbek T, Lin Z, Tan K, Wu Q, Yuan L, Lai J, Zhao H, Song W. Dynamic transcriptome landscape of developing maize ear. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1856-1870. [PMID: 37731154 DOI: 10.1111/tpj.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/19/2023] [Accepted: 08/26/2023] [Indexed: 09/22/2023]
Abstract
Seed number and harvesting ability in maize (Zea mays L.) are primarily determined by the architecture of female inflorescence, namely the ear. Therefore, ear morphogenesis contributes to grain yield and as such is one of the key target traits during maize breeding. However, the molecular networks of this highly dynamic and complex grain-bearing inflorescence remain largely unclear. As a first step toward characterizing these networks, we performed a high-spatio-temporal-resolution investigation of transcriptomes using 130 ear samples collected from developing ears with length from 0.1 mm to 19.0 cm. Comparisons of these mRNA populations indicated that these spatio-temporal transcriptomes were clearly separated into four distinct stages stages I, II, III, and IV. A total of 23 793 genes including 1513 transcription factors (TFs) were identified in the investigated developing ears. During the stage I of ear morphogenesis, 425 genes were predicted to be involved in a co-expression network established by eight hub TFs. Moreover, 9714 ear-specific genes were identified in the seven kinds of meristems. Additionally, 527 genes including 59 TFs were identified as especially expressed in ear and displayed high temporal specificity. These results provide a high-resolution atlas of gene activity during ear development and help to unravel the regulatory modules associated with the differentiation of the ear in maize.
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Affiliation(s)
- Xiaomeng Shen
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Bing Xiao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Tangnur Kaderbek
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Zhen Lin
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Kaiwen Tan
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Qingyu Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Lixing Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
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Dissecting Heterosis During the Ear Inflorescence Development Stage in Maize via a Metabolomics-based Analysis. Sci Rep 2019; 9:212. [PMID: 30659214 PMCID: PMC6338801 DOI: 10.1038/s41598-018-36446-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/13/2018] [Indexed: 11/08/2022] Open
Abstract
Heterosis can increase the yield of many crops and has been extensively applied in agriculture. In maize, female inflorescence architecture directly determines grain yield. Thus, exploring the relationship between early maize ear inflorescence development and heterosis regarding yield-related traits may be helpful for characterizing the molecular mechanisms underlying heterotic performance. In this study, we fine mapped the overdominant heterotic locus (hlEW2b), associated with ear width, in an approximately 1.98-Mb region based on analyses of chromosome segment substitution lines and the corresponding testcross population. Maize ear inflorescences at the floral meristem stage were collected from two inbred lines, one chromosome segment substitution line that carried hlEW2b (sub-CSSL16), the receptor parent lx9801, and the Zheng58 × sub-CSSL16 and Zheng58 × lx9801 hybrid lines. A total of 256 metabolites were identified, including 31 and 24 metabolites that were differentially accumulated between the two hybrid lines and between the two inbred lines, respectively. Most of these metabolites are involved in complex regulatory mechanisms important for maize ear development. For example, nucleotides are basic metabolites affecting cell composition and carbohydrate synthesis. Additionally, nicotinate and nicotinamide metabolism is important for photosynthesis, plant stress responses, and cell expansion. Moreover, flavonoid and phenolic metabolites regulate auxin transport and cell apoptosis. Meanwhile, phytohormone biosynthesis and distribution influence the cell cycle and cell proliferation. Our results revealed that changes in metabolite contents may affect the heterotic performance related to ear width and yield in maize hybrid lines. This study provides new clues in heterosis at the metabolomics level and implies that differentially accumulated metabolites made distinct contributions to the heterosis at an early stage of ear inflorescences development.
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Li Q, Liu B. Genetic regulation of maize flower development and sex determination. PLANTA 2017; 245:1-14. [PMID: 27770199 DOI: 10.1007/s00425-016-2607-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 10/14/2016] [Indexed: 05/23/2023]
Abstract
The determining process of pistil fate are central to maize sex determination, mainly regulated by a genetic network in which the sex-determining genes SILKLESS 1 , TASSEL SEED 1 , TASSEL SEED 2 and the paramutagenic locus Required to maintain repression 6 play pivotal roles. Maize silks, which emerge from the ear shoot and derived from the pistil, are the functional stigmas of female flowers and play a pivotal role in pollination. Previous studies on sex-related mutants have revealed that sex-determining genes and phytohormones play an important role in the regulation of flower organogenesis. The processes determining pistil fate are central to flower development, where a silk identified gene SILKLESS 1 (SK1) is required to protect pistil primordia from a cell death signal produced by two commonly known genes, TASSEL SEED 1 (TS1) and TASSEL SEED 2 (TS2). In this review, maize flower developmental process is presented together with a focus on important sex-determining mutants and hormonal signaling affecting pistil development. The role of sex-determining genes, microRNAs, phytohormones, and the paramutagenic locus Required to maintain repression 6 (Rmr6), in forming a regulatory network that determines pistil fate, is discussed. Cloning SK1 and clarifying its function were crucial in understanding the regulation network of sex determination. The signaling mechanisms of phytohormones in sex determination are also an important research focus.
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Affiliation(s)
- Qinglin Li
- College of Agronomy/State Key Laboratory of Crop Biology, Shandong Agricultural University, Daizong Road No. 61, Taian, 271018, Shandong, China.
| | - Baoshen Liu
- College of Agronomy/State Key Laboratory of Crop Biology, Shandong Agricultural University, Daizong Road No. 61, Taian, 271018, Shandong, China.
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Hu X, Wang H, Diao X, Liu Z, Li K, Wu Y, Liang Q, Wang H, Huang C. Transcriptome profiling and comparison of maize ear heterosis during the spikelet and floret differentiation stages. BMC Genomics 2016; 17:959. [PMID: 27875998 PMCID: PMC5120533 DOI: 10.1186/s12864-016-3296-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 11/15/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hybridization is a prominent process in the evolution of crop plants that can give rise to gene expression variation, phenotypic novelty and heterosis. Maize is the most successful crop in utilizing heterosis. The development of hybrid maize ears exhibits strong heterotic vigor and greatly affects maize yield. However, a comprehensive perspective on transcriptional variation and its correlation with heterosis during maize ear development is not available. RESULTS Using RNA sequencing technology, we investigated the transcriptome profiles of maize ears in the spikelet and floret differentiation stages of hybrid ZD808 and its parents CL11 and NG5. Our results revealed that 53.9% (21,258) of maize protein-coding genes were transcribed in at least one genotype. In both development stages, significant numbers of genes were differentially expressed between the hybrid and its parents. Gene expression inheritance analysis revealed approximately 80% of genes were expressed additively, which suggested that the complementary effect may play a foundation role in maize ear heterosis. Among non-additively expressed genes, NG5-dominant genes were predominant. Analyses of the allele-specific gene expression in hybrid identified pervasive allelic imbalance and significant preferential expression of NG5 alleles in both developmental stages. The results implied that NG5 may provide beneficial alleles that contribute greatly to heterosis. Further comparison of parental and hybrid allele-specific expression suggested that gene expression variation is largely attributable to cis-regulatory variation in maize. The cis-regulatory variations tend to preserve the allelic expression levels in hybrid and result in additive expression. Comparison between the two development stages revealed that allele-specific expression and cis-/trans-regulatory variations responded differently to developmental cues, which may lead to stage-specific vigor phenotype during maize ear development. CONCLUSION Our research suggests that cis-regulated additive expression may fine-tune gene expression level into an optimal status and play a foundation role in maize ear heterosis. Our work provides a comprehensive insight into transcriptional variation and its correlation with heterosis during maize ear development. The knowledge gained from this study presents novel opportunity to improve our maize varieties.
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Affiliation(s)
- Xiaojiao Hu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Hongwu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Xizhou Diao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Zhifang Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Kun Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Yujin Wu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Qianjin Liang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Hui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
| | - Changling Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Main Street, Beijing, 100081 China
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Sobral R, Silva HG, Morais-Cecílio L, Costa MMR. The Quest for Molecular Regulation Underlying Unisexual Flower Development. FRONTIERS IN PLANT SCIENCE 2016; 7:160. [PMID: 26925078 PMCID: PMC4759290 DOI: 10.3389/fpls.2016.00160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/30/2016] [Indexed: 05/16/2023]
Abstract
The understanding of the molecular mechanisms responsible for the making of a unisexual flower has been a long-standing quest in plant biology. Plants with male and female flowers can be divided mainly into two categories: dioecious and monoecious, and both sexual systems co-exist in nature in ca of 10% of the angiosperms. The establishment of male and female traits has been extensively described in a hermaphroditic flower and requires the interplay of networks, directly and indirectly related to the floral organ identity genes including hormonal regulators, transcription factors, microRNAs, and chromatin-modifying proteins. Recent transcriptomic studies have been uncovering the molecular processes underlying the establishment of unisexual flowers and there are many parallelisms between monoecious, dioecious, and hermaphroditic individuals. Here, we review the paper entitled "Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber" published in 2014 in the Frontiers of Plant Science (volume 5 |Article 599) and discussed it in the context of recent studies with other dioecious and monoecious plants that utilized high-throughput platforms to obtain transcriptomic profiles of male and female unisexual flowers. In some unisexual flowers, the developmental programs that control organ initiation fail and male or female organs do not form, whereas in other species, organ initiation and development occur but they abort or arrest during different species-specific stages of differentiation. Therefore, a direct comparison of the pathways responsible for the establishment of unisexual flowers in different species are likely to reveal conserved modules of gene regulatory hubs involved in stamen or carpel development, as well as differences that reflect the different stages of development in which male and/or female organ arrest or loss-of-function occurs.
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Affiliation(s)
- Rómulo Sobral
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Helena G. Silva
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Leonor Morais-Cecílio
- Departamento de Recursos Naturais Ambiente e Território, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Maria M. R. Costa
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
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Wang T, Sui Z, Liu X, Li Y, Li H, Xing J, Song F, Zhang Y, Sun Q, Ni Z. Ectopic expression of a maize hybrid up-regulated gene, ErbB-3 binding Protein 1 (ZmEBP1), increases organ size by promoting cell proliferation in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 243:23-34. [PMID: 26795148 DOI: 10.1016/j.plantsci.2015.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 05/21/2023]
Abstract
The alteration of gene expression in hybrids may be an important factor promoting phenotypic variation and plasticity. To provide insight into the underlying molecular basis of maize heterosis in terms of the kernel number per ear, we established DGE profiles for the immature ears of maize hybrid Zong3/87-1 and its parental lines at the floral organ differentiation stage. Among 4,337 identified differentially expressed genes, 4,021 (92%) exhibited nonadditive expression patterns in the hybrid. Notably, the maize homolog of Arabidopsis EBP1, designated ZmEBP1, displayed an overdominant expression pattern in the Zong3/87-1 hybrid. Moreover, the results of qRT-PCR revealed that the ZmEBP1 gene was upregulated in the immature ears of the reciprocal hybrids Zong3/87-1 and 87-1/Zong3 at different developmental stages. Additionally, ectopic expression of ZmEBP1 in Arabidopsis increased organ size, which was mainly attributed to an increase in cell numbers, rather than cell size. Considering all of these findings together, we speculate that upregulation of ZmEBP1 in maize hybrids may accelerate cell proliferation and promote ear development.
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Affiliation(s)
- Tianya Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Yangyang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Hongjian Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Fangwei Song
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Yirong Zhang
- National Maize Improvement Centre of China, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; National Plant Gene Research Centre (Beijing), Beijing 100193, China.
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Pan X, Hasan MM, Li Y, Liao C, Zheng H, Liu R, Li X. Asymmetric transcriptomic signatures between the cob and florets in the maize ear under optimal- and low-nitrogen conditions at silking, and functional characterization of amino acid transporters ZmAAP4 and ZmVAAT3. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6149-66. [PMID: 26136266 PMCID: PMC4588875 DOI: 10.1093/jxb/erv315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Coordinated functioning of the cob and florets of the maize ear confers grain yield. The cob is critical for carbon partitioning and assimilated nitrogen (N) supply for grain development. However, molecular recognition of the cob and peripheral florets, characterization of genes mediating translocation of N assimilates, and responses of these two tissues to low N (LN) remain elusive. Transcriptional profiling of the ear of a maize hybrid at silking in the field revealed 1864 differentially expressed genes between the cob and florets, with 1314 genes up-regulated in the cob and 550 genes up-regulated in florets. The cob was characterized by striking enrichment of genes that are involved in carbon/N transport and metabolism, consistent with the physiological role of the cob in carbon/N storage and transfer during ear development. The florets were characterized by enrichment of hormone signalling components and development related genes. We next examined the response of the cob and florets to LN stress. LN caused differential expression of 588 genes in the cob and only 195 genes in the florets, indicating that the cob dominated the response of the ear to LN at the transcriptional level. LN caused comprehensive alterations such as carbon/N metabolism or partitioning, hormone signalling and protein phosphorylation in terms of gene expression in the cob and/or florets. Fourteen genes responsive specifically to LN provided potential molecular markers for N-efficient maize breeding. We further functionally characterized two newly identified broad-spectrum amino acid transporters, ZmAAP4 and ZmVAAT3, that showed distinct expression patterns in the cob and florets and potentially important roles in amino-N mobilization in the ear. While both proteins could transport various amino acids into yeast or Arabidopsis cells, ZmAAP4 appeared to have higher efficiencies than ZmVAAT3 in transporting seven out of 22 examined amino acids.
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Affiliation(s)
- Xiaoying Pan
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China
| | - Md Mahmudul Hasan
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China
| | - Yanqiang Li
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chengsong Liao
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China
| | - Hongyan Zheng
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xuexian Li
- Department of Plant Nutrition, China Agricultural University, Beijing 100193, China
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Liu H, Yang X, Liao X, Zuo T, Qin C, Cao S, Dong L, Zhou H, Zhang Y, Liu S, Shen Y, Lin H, Lübberstedt T, Zhang Z, Pan G. Genome-wide comparative analysis of digital gene expression tag profiles during maize ear development. Genomics 2015; 106:52-60. [PMID: 25847872 DOI: 10.1016/j.ygeno.2015.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 11/30/2022]
Abstract
The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutant analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.
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Affiliation(s)
- Hongjun Liu
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Xuerong Yang
- Institute of Animal Nutrition, Sichuan Agricultural University, Ya'an 625014, China
| | | | - Tao Zuo
- Interdepartmental Genetics Program, Iowa State University, Ames 50011, USA
| | - Cheng Qin
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China; Zunyi Academy of Agricultural Sciences, Zunyi 563102, China
| | - Shiliang Cao
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, 150086 Harbin, China
| | - Ling Dong
- Department of Agronomy, Northeast Agricultural University, 150030 Harbin, China
| | | | - Yongzhong Zhang
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Sisi Liu
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yaou Shen
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | | | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
| | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University, Chengdu 611130, China.
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9
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Yu T, Wang Z, Jin X, Liu X, Kan S. Analysis of gene expression profiles in response to Sporisorium reilianum f. sp. zeae in maize (Zea mays L.). ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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10
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Ding H, Qin C, Luo X, Li L, Chen Z, Liu H, Gao J, Lin H, Shen Y, Zhao M, Lübberstedt T, Zhang Z, Pan G. Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid. Int J Mol Sci 2014; 15:13892-915. [PMID: 25116687 PMCID: PMC4159830 DOI: 10.3390/ijms150813892] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 12/15/2022] Open
Abstract
Heterosis, or hybrid vigor, contributes to superior agronomic performance of hybrids compared to their inbred parents. Despite its importance, little is known about the genetic and molecular basis of heterosis. Early maize ear inflorescences formation affects grain yield, and are thus an excellent model for molecular mechanisms involved in heterosis. To determine the parental contributions and their regulation during maize ear-development-genesis, we analyzed genome-wide digital gene expression profiles in two maize elite inbred lines (B73 and Mo17) and their F1 hybrid using deep sequencing technology. Our analysis revealed 17,128 genes expressed in these three genotypes and 22,789 genes expressed collectively in the present study. Approximately 38% of the genes were differentially expressed in early maize ear inflorescences from heterotic cross, including many transcription factor genes and some presence/absence variations (PAVs) genes, and exhibited multiple modes of gene action. These different genes showing differential expression patterns were mainly enriched in five cellular component categories (organelle, cell, cell part, organelle part and macromolecular complex), five molecular function categories (structural molecule activity, binding, transporter activity, nucleic acid binding transcription factor activity and catalytic activity), and eight biological process categories (cellular process, metabolic process, biological regulation, regulation of biological process, establishment of localization, cellular component organization or biogenesis, response to stimulus and localization). Additionally, a significant number of genes were expressed in only one inbred line or absent in both inbred lines. Comparison of the differences of modes of gene action between previous studies and the present study revealed only a small number of different genes had the same modes of gene action in both maize seedlings and ear inflorescences. This might be an indication that in different tissues or developmental stages, different global expression patterns prevail, which might nevertheless be related to heterosis. Our results support the hypotheses that multiple molecular mechanisms (dominance and overdominance modes) contribute to heterosis.
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Affiliation(s)
- Haiping Ding
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Cheng Qin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China; E-Mail:
| | - Xirong Luo
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China; E-Mail:
| | - Lujiang Li
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Zhe Chen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Hongjun Liu
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Jian Gao
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Yaou Shen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Maojun Zhao
- Life Science College, Sichuan Agricultural University, Ya’an 625014, China; E-Mail:
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; E-Mail:
| | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Authors to whom correspondence should be addressed; E-Mails: (Z.Z.); (G.P.); Tel.: +86-28-8629-0917 (G.P.); Fax: +86-28-8629-0916 (G.P.)
| | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Authors to whom correspondence should be addressed; E-Mails: (Z.Z.); (G.P.); Tel.: +86-28-8629-0917 (G.P.); Fax: +86-28-8629-0916 (G.P.)
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Tran F, Penniket C, Patel RV, Provart NJ, Laroche A, Rowland O, Robert LS. Developmental transcriptional profiling reveals key insights into Triticeae reproductive development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:971-88. [PMID: 23581995 DOI: 10.1111/tpj.12206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/15/2013] [Accepted: 03/22/2013] [Indexed: 05/25/2023]
Abstract
Despite their importance, there remains a paucity of large-scale gene expression-based studies of reproductive development in species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip(®) wheat genome array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages, and co-expressed as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function. This comprehensive resource rests upon detailed gene annotations, and the expression profiles are readily accessible via a web browser.
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Affiliation(s)
- Frances Tran
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
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12
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Jiménez-López S, Mancera-Martínez E, Donayre-Torres A, Rangel C, Uribe L, March S, Jiménez-Sánchez G, Sánchez de Jiménez E. Expression profile of maize (Zea mays L.) embryonic axes during germination: translational regulation of ribosomal protein mRNAs. PLANT & CELL PHYSIOLOGY 2011; 52:1719-33. [PMID: 21880676 DOI: 10.1093/pcp/pcr114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Seed germination is a critical developmental period for plant propagation. Information regarding gene expression within this important period is relevant for understanding the main biochemical processes required for successful germination, particularly in maize, one of the most important cereals in the world. The present research focuses on the global microarray analysis of differential gene expression between quiescent and germinated maize embryo stages. This analysis revealed that a large number of mRNAs stored in the quiescent embryonic axes (QEAs) were differentially regulated during germination in the 24 h germinated embryonic axes (GEAs). These genes belong to 14 different functional categories and most of them correspond to metabolic processes, followed by transport, transcription and translation. Interestingly, the expression of mRNAs encoding ribosomal proteins [(r)-proteins], required for new ribosome formation during this fast-growing period, remains mostly unchanged throughout the germination process, suggesting that these genes are not regulated at the transcriptional level during this developmental period. To investigate this issue further, comparative microarray analyses on polysomal mRNAs from growth-stimulated and non-stimulated GEAs were performed. The results revealed that (r)-protein mRNAs accumulate to high levels in polysomes of the growth-stimulated tissues, indicating a translational control mechanism to account for the rapid (r)-protein synthesis observed within this period. Bioinformatic analysis of (r)-protein mRNAs showed that 5' TOP (tract of pyrimidines)-like sequences are present only in the 5'-untranslated region set of up-regulated (r)-protein mRNAs. This overall approach to the germination process allows an in-depth view of molecular changes, enabling a broader understanding of the regulatory mechanisms that occur during this process.
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Affiliation(s)
- Sara Jiménez-López
- Biochemistry Department, Faculty of Chemistry, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad Universitaria, 04510 Mexico, D.F. México
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13
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Fu J, Thiemann A, Schrag TA, Melchinger AE, Scholten S, Frisch M. Dissecting grain yield pathways and their interactions with grain dry matter content by a two-step correlation approach with maize seedling transcriptome. BMC PLANT BIOLOGY 2010; 10:63. [PMID: 20385002 PMCID: PMC2923537 DOI: 10.1186/1471-2229-10-63] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 04/12/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND The importance of maize for human and animal nutrition, but also as a source for bio-energy is rapidly increasing. Maize yield is a quantitative trait controlled by many genes with small effects, spread throughout the genome. The precise location of the genes and the identity of the gene networks underlying maize grain yield is unknown. The objective of our study was to contribute to the knowledge of these genes and gene networks by transcription profiling with microarrays. RESULTS We assessed the grain yield and grain dry matter content (an indicator for early maturity) of 98 maize hybrids in multi-environment field trials. The gene expression in seedlings of the parental inbred lines, which have four different genetic backgrounds, was assessed with genome-scale oligonucleotide arrays. We identified genes associated with grain yield and grain dry matter content using a newly developed two-step correlation approach and found overlapping gene networks for both traits. The underlying metabolic pathways and biological processes were elucidated. Genes involved in sucrose degradation and glycolysis, as well as genes involved in cell expansion and endocycle were found to be associated with grain yield. CONCLUSIONS Our results indicate that the capability of providing energy and substrates, as well as expanding the cell at the seedling stage, highly influences the grain yield of hybrids. Knowledge of these genes underlying grain yield in maize can contribute to the development of new high yielding varieties.
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Affiliation(s)
- Junjie Fu
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
| | | | - Tobias A Schrag
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Albrecht E Melchinger
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Stefan Scholten
- Biocenter Klein Flottbek, University of Hamburg, 22609 Hamburg, Germany
| | - Matthias Frisch
- Institute of Agronomy and Plant Breeding II, Justus Liebig University, 35392 Giessen, Germany
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Wang L, Li P, Brutnell TP. Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct Genomics 2010; 9:118-28. [PMID: 20130067 DOI: 10.1093/bfgp/elp057] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Ultra high-throughput sequencing (UHTS) technologies offer the potential to interrogate transcriptomes in detail that has traditionally been restricted to single gene surveys. For instance, it is now possible to globally define transcription start sites, polyadenylation signals, alternative splice sites and generate quantitative data on gene transcript accumulation in single tissues or cell types. These technologies are thus paving the way for whole genome transcriptomics and will undoubtedly lead to novel insights into plant development and biotic and abiotic stress responses. However, several challenges exist to making this technology broadly accessible to the plant research community. These include the current need for a computationally intensive analysis of data sets, a lack of standardized alignment and formatting procedures and a relatively small number of analytical software packages to interpret UHTS outputs. In this review we summarize recent findings from UHTS and discuss potential opportunities and challenges for broad adoption of these technologies in the plant science community.
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Affiliation(s)
- Lin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
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