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Farooqi MQU, Nawaz G, Wani SH, Choudhary JR, Rana M, Sah RP, Afzal M, Zahra Z, Ganie SA, Razzaq A, Reyes VP, Mahmoud EA, Elansary HO, El-Abedin TKZ, Siddique KHM. Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2022; 13:965878. [PMID: 36212378 PMCID: PMC9538355 DOI: 10.3389/fpls.2022.965878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/23/2022] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing technologies (HSTs) have revolutionized crop breeding. The advent of these technologies has enabled the identification of beneficial quantitative trait loci (QTL), genes, and alleles for crop improvement. Climate change have made a significant effect on the global maize yield. To date, the well-known omic approaches such as genomics, transcriptomics, proteomics, and metabolomics are being incorporated in maize breeding studies. These approaches have identified novel biological markers that are being utilized for maize improvement against various abiotic stresses. This review discusses the current information on the morpho-physiological and molecular mechanism of abiotic stress tolerance in maize. The utilization of omics approaches to improve abiotic stress tolerance in maize is highlighted. As compared to single approach, the integration of multi-omics offers a great potential in addressing the challenges of abiotic stresses of maize productivity.
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Affiliation(s)
| | - Ghazala Nawaz
- Department of Botanical and Environmental Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jeet Ram Choudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Maneet Rana
- Division of Crop Improvement, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rameswar Prasad Sah
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - Muhammad Afzal
- College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Zahra Zahra
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA, United States
| | | | - Ali Razzaq
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | | | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta, Egypt
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
- Floriculture, Ornamental Horticulture, and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
- Department of Geography, Environmental Management, and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Tarek K. Zin El-Abedin
- Department of Agriculture & Biosystems Engineering, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
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Lian T, Wang X, Li S, Jiang H, Zhang C, Wang H, Jiang L. Comparative Transcriptome Analysis Reveals Mechanisms of Folate Accumulation in Maize Grains. Int J Mol Sci 2022; 23:ijms23031708. [PMID: 35163628 PMCID: PMC8836222 DOI: 10.3390/ijms23031708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/05/2023] Open
Abstract
Previously, the complexity of folate accumulation in the early stages of maize kernel development has been reported, but the mechanisms of folate accumulation are unclear. Two maize inbred lines, DAN3130 and JI63, with different patterns of folate accumulation and different total folate contents in mature kernels were used to investigate the transcriptional regulation of folate metabolism during late stages of kernel formation by comparative transcriptome analysis. The folate accumulation during DAP 24 to mature kernels could be controlled by circumjacent pathways of folate biosynthesis, such as pyruvate metabolism, glutamate metabolism, and serine/glycine metabolism. In addition, the folate variation between these two inbred lines was related to those genes among folate metabolism, such as genes in the pteridine branch, para-aminobenzoate branch, serine/tetrahydrofolate (THF)/5-methyltetrahydrofolate cycle, and the conversion of THF monoglutamate to THF polyglutamate. The findings provided insight into folate accumulation mechanisms during maize kernel formation to promote folate biofortification.
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Affiliation(s)
- Tong Lian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Xuxia Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Sha Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
| | - Haiyang Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (X.W.); (H.J.)
- National Agricultural Science and Technology Center, Chengdu 610213, China
- Correspondence: (H.W.); (L.J.)
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.L.); (S.L.); (C.Z.)
- Correspondence: (H.W.); (L.J.)
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3
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Motto M, Sahay S. Energy plants (crops): potential natural and future designer plants. HANDBOOK OF BIOFUELS 2022:73-114. [DOI: 10.1016/b978-0-12-822810-4.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Volokhina I, Gusev Y, Moiseeva Y, Gutorova O, Fadeev V, Chumakov M. Gene Expression in Parthenogenic Maize Proembryos. PLANTS (BASEL, SWITZERLAND) 2021; 10:964. [PMID: 34066123 PMCID: PMC8151209 DOI: 10.3390/plants10050964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Angiosperm plants reproduce both sexually and asexually (by apomixis). In apomictic plants, the embryo and endosperm develop without fertilization. Modern maize seems to have a broken apomixis-triggering mechanism, which still works in Tripsacum and in Tripsacum-maize hybrids. For the first time, maize lines characterized by pronounced and inheritable high-frequency maternal parthenogenesis were generated 40 years ago, but there are no data on gene expression in parthenogenic maize proembryos. Here we examined for the first time gene expression in parthenogenic proembryos isolated from unpollinated embryo sacs (ESs) of a parthenogenic maize line (AT-4). The DNA-methylation genes (dmt103, dmt105) and the genes coding for the chromatin-modifying enzymes (chr106, hdt104, hon101) were expressed much higher in parthenogenic proembryos than in unpollinated ESs. The expression of the fertilization-independent endosperm (fie1) genes was found for the first time in parthenogenic proembryos and unpollinated ESs. In parthenogenic proembryos, the Zm_fie2 gene was expressed up to two times higher than it was expressed in unpollinated ESs.
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Affiliation(s)
- Irina Volokhina
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Yury Gusev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Yelizaveta Moiseeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Olga Gutorova
- Genetics Department, Saratov State University, 83 Ulitsa Astrakhanskaya, 410012 Saratov, Russia;
| | - Vladimir Fadeev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
| | - Mikhail Chumakov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, 410049 Saratov, Russia; (I.V.); (Y.G.); (Y.M.); (V.F.)
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Daba SD, Liu X, Aryal U, Mohammadi M. A proteomic analysis of grain yield-related traits in wheat. AOB PLANTS 2020; 12:plaa042. [PMID: 33133478 PMCID: PMC7586745 DOI: 10.1093/aobpla/plaa042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/19/2020] [Indexed: 05/13/2023]
Abstract
Grain yield, which is mainly contributed by tillering capacity as well as kernel number and weight, is the most important trait to plant breeders and agronomists. Label-free quantitative proteomics was used to analyse yield-contributing organs in wheat. These were leaf sample, tiller initiation, spike initiation, ovary and three successive kernel development stages at 5, 10 and 15 days after anthesis (DAA). We identified 3182 proteins across all samples. The largest number was obtained for spike initiation (1673), while the smallest was kernel sample at 15 DAA (709). Of the 3182 proteins, 296 of them were common to all seven organs. Organ-specific proteins ranged from 148 in ovary to 561 in spike initiation. When relative protein abundances were compared to that of leaf sample, 347 and 519 proteins were identified as differentially abundant in tiller initiation and spike initiation, respectively. When compared with ovary, 81, 35 and 96 proteins were identified as differentially abundant in kernels sampled at 5, 10 and 15 DAA, respectively. Our study indicated that two Argonaute proteins were solely expressed in spike initiation. Of the four expansin proteins detected, three of them were mainly expressed during the first 10 days of kernel development after anthesis. We also detected cell wall invertases and sucrose and starch synthases mainly during the kernel development period. The manipulation of these proteins could lead to increases in tillers, kernels per spike or final grain weight, and is worth exploring in future studies.
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Affiliation(s)
- Sintayehu D Daba
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Xiaoqin Liu
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Uma Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
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SNP-based mixed model association of growth- and yield-related traits in popcorn. PLoS One 2019; 14:e0218552. [PMID: 31237892 PMCID: PMC6592533 DOI: 10.1371/journal.pone.0218552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022] Open
Abstract
The identification of the genes responsible for complex traits is highly promising to accelerate crop breeding, but such information is still limited for popcorn. Thus, in the present study, a mixed linear model-based association analysis (MLMA) was applied for six important popcorn traits: plant and ear height, 100-grain weight, popping expansion, grain yield and expanded popcorn volume per hectare. To this end, 196 plants of the open-pollinated popcorn population UENF-14 were sampled, selfed (S1), and then genotyped with a panel of 10,507 single nucleotide polymorphisms (SNPs) markers distributed throughout the genome. The six traits were studied under two environments [Campos dos Goytacazes-RJ (ENV1) and Itaocara-RJ (ENV2)] in an incomplete block design. Based on the phenotypic data of the S1 progenies and on the genetic characteristics of the parents, the MLMA was performed. Thereafter, genes annotated in the MaizeGDB platform were screened for potential linkage disequilibrium with the SNPs associated to the six evaluated traits. Overall, seven and eight genes were identified as associated with the traits in ENV1 and ENV2, respectively, and proteins encoded by these genes were evaluated for their function. The results obtained here contribute to increase knowledge on the genetic architecture of the six evaluated traits and might be used for marker-assisted selection in breeding programs.
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Zheng L, Zhang X, Zhang H, Gu Y, Huang X, Huang H, Liu H, Zhang J, Hu Y, Li Y, Yu G, Liu Y, Lawson SS, Huang Y. The miR164-dependent regulatory pathway in developing maize seed. Mol Genet Genomics 2019; 294:501-517. [DOI: 10.1007/s00438-018-1524-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023]
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8
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Kang SH, Lee JY, Lee TH, Park SY, Kim CK. De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing. PLoS One 2018; 13:e0208344. [PMID: 30533012 PMCID: PMC6289447 DOI: 10.1371/journal.pone.0208344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022] Open
Abstract
Adlay (Coix lacryma-jobi) is a tropical grass that has long been used in traditional Chinese medicine and is known for its nutritional benefits. Recent studies have shown that vitamin E compounds in adlay protect against chronic diseases such as cancer and heart disease. However, the molecular basis of adlay's health benefits remains unknown. Here, we generated adlay gene sets by de novo transcriptome assembly using long-read isoform sequencing (Iso-Seq) and short-read RNA-Sequencing (RNA-Seq). The gene sets obtained from Iso-seq and RNA-seq contained 31,177 genes and 57,901 genes, respectively. We confirmed the validity of the assembled gene sets by experimentally analyzing the levels of prolamin and vitamin E biosynthesis-associated proteins in adlay plant tissues and seeds. We compared the screened adlay genes with known gene families from closely related plant species, such as rice, sorghum and maize. We also identified tissue-specific genes from the adlay leaf, root, and young and mature seed, and experimentally validated the differential expression of 12 randomly-selected genes. Our study of the adlay transcriptome will provide a valuable resource for genetic studies that can enhance adlay breeding programs in the future.
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Affiliation(s)
- Sang-Ho Kang
- International Technology Cooperation Center, RDA, Jeonju, Republic of Korea
| | - Jong-Yeol Lee
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju, Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, Korea
| | - Soo-Yun Park
- Biosafety Division, National Institute of Agricultural Sciences, RDA, Jeonju, Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, Korea
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Liu L, Liu J. Inferring gene regulatory networks with hybrid of multi-agent genetic algorithm and random forests based on fuzzy cognitive maps. Appl Soft Comput 2018. [DOI: 10.1016/j.asoc.2018.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Xiong W, Wang C, Zhang X, Yang Q, Shao R, Lai J, Du C. Highly interwoven communities of a gene regulatory network unveil topologically important genes for maize seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1143-1156. [PMID: 29072883 DOI: 10.1111/tpj.13750] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/10/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
The complex interactions between transcription factors (TFs) and their target genes in a spatially and temporally specific manner are crucial to all cellular processes. Reconstruction of gene regulatory networks (GRNs) from gene expression profiles can help to decipher TF-gene regulations in a variety of contexts; however, the inevitable prediction errors of GRNs hinder optimal data mining of RNA-Seq transcriptome profiles. Here we perform an integrative study of Zea mays (maize) seed development in order to identify key genes in a complex developmental process. First, we reverse engineered a GRN from 78 maize seed transcriptome profiles. Then, we studied collective gene interaction patterns and uncovered highly interwoven network communities as the building blocks of the GRN. One community, composed of mostly unknown genes interacting with opaque2, brittle endosperm1 and shrunken2, contributes to seed phenotypes. Another community, composed mostly of genes expressed in the basal endosperm transfer layer, is responsible for nutrient transport. We further integrated our inferred GRN with gene expression patterns in different seed compartments and at various developmental stages and pathways. The integration facilitated a biological interpretation of the GRN. Our yeast one-hybrid assays verified six out of eight TF-promoter bindings in the reconstructed GRN. This study identified topologically important genes in interwoven network communities that may be crucial to maize seed development.
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Affiliation(s)
- Wenwei Xiong
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA
| | - Chunlei Wang
- National Maize Improvement Center, China Agricultural University, Beijing, 100083, China
| | - Xiangbo Zhang
- National Maize Improvement Center, China Agricultural University, Beijing, 100083, China
| | - Qinghua Yang
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ruixin Shao
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jinsheng Lai
- National Maize Improvement Center, China Agricultural University, Beijing, 100083, China
| | - Chunguang Du
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA
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Xu X, Wang M, Li L, Che R, Li P, Pei L, Li H. Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels. BMC PLANT BIOLOGY 2017; 17:163. [PMID: 29037150 PMCID: PMC5644097 DOI: 10.1186/s12870-017-1119-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Dissecting the genetic basis and regulatory mechanisms for the biosynthesis and accumulation of nutrients in maize could lead to the improved nutritional quality of this crop. Gene expression is regulated at the genomic, transcriptional, and post-transcriptional levels, all of which can produce diversity among traits. However, the expression of most genes connected with a particular trait usually does not have a direct association with the variation of that trait. In addition, expression profiles of genes involved in a single pathway may vary as the intrinsic cellular state changes. To work around these issues, we utilized a statistical method, liquid association (LA) to investigate the complex pattern of gene regulation in maize kernels. RESULTS We applied LA to the expression profiles of 28,769 genes to dissect dynamic trait-trait correlation patterns in maize kernels. Among the 1000 LA pairs (LAPs) with the largest LA scores, 686 LAPs were identified conditional correlation. We also identified 830 and 215 LA-scouting leaders based on the positive and negative LA scores, which were significantly enriched for some biological processes and molecular functions. Our analysis of the dynamic co-expression patterns in the carotene biosynthetic pathway clearly indicated the important role of lcyE, CYP97A, ZEP1, and VDE in this pathway, which may change the direction of carotene biosynthesis by controlling the influx and efflux of the substrate. The dynamic trait-trait correlation patterns between gene expression and oil concentration in the fatty acid metabolic pathway and its complex regulatory network were also assessed. 23 of 26 oil-associated genes were correlated with oil concentration conditioning on 580 LA-scoutinggenes, and 5% of these LA-scouting genes were annotated as enzymes in the oil metabolic pathway. CONCLUSIONS By focusing on the carotenoid and oil biosynthetic pathways in maize, we showed that a genome-wide LA analysis provides a novel and effective way to detect transcriptional regulatory relationships. This method will help us understand the biological role of maize kernel genes and will benefit maize breeding programs.
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Affiliation(s)
- Xiuqin Xu
- School of Biological and Science Technology, University of Jinan, Jinan, 250022 China
| | - Min Wang
- National Maize Improvement Center of China, Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Lianbo Li
- School of Biological and Science Technology, University of Jinan, Jinan, 250022 China
| | - Ronghui Che
- School of Biological and Science Technology, University of Jinan, Jinan, 250022 China
| | - Peng Li
- School of Biological and Science Technology, University of Jinan, Jinan, 250022 China
| | - Laming Pei
- School of Biological and Science Technology, University of Jinan, Jinan, 250022 China
| | - Hui Li
- School of Biological and Science Technology, University of Jinan, Jinan, 250022 China
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Doll NM, Depège-Fargeix N, Rogowsky PM, Widiez T. Signaling in Early Maize Kernel Development. MOLECULAR PLANT 2017; 10:375-388. [PMID: 28267956 DOI: 10.1016/j.molp.2017.01.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 05/26/2023]
Abstract
Developing the next plant generation within the seed requires the coordination of complex programs driving pattern formation, growth, and differentiation of the three main seed compartments: the embryo (future plant), the endosperm (storage compartment), representing the two filial tissues, and the surrounding maternal tissues. This review focuses on the signaling pathways and molecular players involved in early maize kernel development. In the 2 weeks following pollination, functional tissues are shaped from single cells, readying the kernel for filling with storage compounds. Although the overall picture of the signaling pathways regulating embryo and endosperm development remains fragmentary, several types of molecular actors, such as hormones, sugars, or peptides, have been shown to be involved in particular aspects of these developmental processes. These molecular actors are likely to be components of signaling pathways that lead to transcriptional programming mediated by transcriptional factors. Through the integrated action of these components, multiple types of information received by cells or tissues lead to the correct differentiation and patterning of kernel compartments. In this review, recent advances regarding the four types of molecular actors (hormones, sugars, peptides/receptors, and transcription factors) involved in early maize development are presented.
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Affiliation(s)
- Nicolas M Doll
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Nathalie Depège-Fargeix
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Peter M Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France.
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Transcriptome Dynamics during Maize Endosperm Development. PLoS One 2016; 11:e0163814. [PMID: 27695101 PMCID: PMC5047526 DOI: 10.1371/journal.pone.0163814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/14/2016] [Indexed: 11/19/2022] Open
Abstract
The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq) analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP). We found that more than 11,000 protein-coding genes underwent alternative splicing (AS) events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs), were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.
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Li D, Liu Z, Gao L, Wang L, Gao M, Jiao Z, Qiao H, Yang J, Chen M, Yao L, Liu R, Kan Y. Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L. PLoS One 2016; 11:e0153168. [PMID: 27082634 PMCID: PMC4833412 DOI: 10.1371/journal.pone.0153168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/24/2016] [Indexed: 11/23/2022] Open
Abstract
The development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels, and miRNAs play important roles during this process. Although a number of miRNAs have been identified in maize seed, the ones involved in the early development of grains and in different lines of maize have not been well studied. Here, we profiled four small RNA libraries, each constructed from groups of immature grains of Zea mays inbred line Chang 7–2 collected 4–6, 7–9, 12–14, and 18–23 days after pollination (DAP). A total of 40 known (containing 111 unique miRNAs) and 162 novel (containing 196 unique miRNA candidates) miRNA families were identified. For conserved and novel miRNAs with over 100 total reads, 44% had higher accumulation before the 9th DAP, especially miR166 family members. 42% of miRNAs had highest accumulation during 12–14 DAP (which is the transition stage from embryogenesis to nutrient storage). Only 14% of miRNAs had higher expression 18–23 DAP. Prediction of potential targets of all miRNAs showed that 165 miRNA families had 377 target genes. For miR164 and miR166, we showed that the transcriptional levels of their target genes were significantly decreased when co-expressed with their cognate miRNA precursors in vivo. Further analysis shows miR159, miR164, miR166, miR171, miR390, miR399, and miR529 families have putative roles in the embryogenesis of maize grain development by participating in transcriptional regulation and morphogenesis, while miR167 and miR528 families participate in metabolism process and stress response during nutrient storage. Our study is the first to present an integrated dynamic expression pattern of miRNAs during maize kernel formation and maturation.
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Affiliation(s)
- Dandan Li
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zongcai Liu
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lei Gao
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Lifang Wang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Meijuan Gao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zhujin Jiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Huili Qiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Jianwei Yang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Min Chen
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- * E-mail: (RYL); (YCK)
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
- * E-mail: (RYL); (YCK)
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15
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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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16
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Zhang Z, Wu X, Shi C, Wang R, Li S, Wang Z, Liu Z, Xue Y, Tang G, Tang J. Genetic dissection of the maize kernel development process via conditional QTL mapping for three developing kernel-related traits in an immortalized F2 population. Mol Genet Genomics 2015; 291:437-54. [DOI: 10.1007/s00438-015-1121-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 09/18/2015] [Indexed: 10/23/2022]
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17
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Lian T, Guo W, Chen M, Li J, Liang Q, Liu F, Meng H, Xu B, Chen J, Zhang C, Jiang L. Genome-wide identification and transcriptional analysis of folate metabolism-related genes in maize kernels. BMC PLANT BIOLOGY 2015; 15:204. [PMID: 26283542 PMCID: PMC4539672 DOI: 10.1186/s12870-015-0578-2] [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] [Received: 03/23/2015] [Accepted: 07/23/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Maize is a major staple food crop globally and contains various concentrations of vitamins. Folates are essential water-soluble B-vitamins that play an important role as one-carbon (C1) donors and acceptors in organisms. To gain an understanding of folate metabolism in maize, we performed an intensive in silico analysis to screen for genes involved in folate metabolism using publicly available databases, followed by examination of the transcript expression patterns and profiling of the folate derivatives in the kernels of two maize inbred lines. RESULTS A total of 36 candidate genes corresponding to 16 folate metabolism-related enzymes were identified. The maize genome contains all the enzymes required for folate and C1 metabolism, characterized by highly conserved functional domains across all the other species investigated. Phylogenetic analysis revealed that these enzymes in maize are conserved throughout evolution and have a high level of similarity with those in sorghum and millet. The LC-MS analyses of two maize inbred lines demonstrated that 5-methyltetrahydrofolate was the major form of folate derivative in young seeds, while 5-formyltetrahydrofolate in mature seeds. Most of the genes involved in folate and C1 metabolism exhibited similar transcriptional expression patterns between these two maize lines, with the highest transcript abundance detected on day after pollination (DAP) 6 and the decreased transcript abundance on DAP 12 and 18. Compared with the seeds on DAP 30, 5-methyltetrahydrofolate was decreased and 5-formyltetrahydrofolate was increased sharply in the mature dry seeds. CONCLUSIONS The enzymes involved in folate and C1 metabolism are conserved between maize and other plant species. Folate and C1 metabolism is active in young developing maize seeds at transcriptional levels.
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Affiliation(s)
- Tong Lian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Wenzhu Guo
- Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Maoran Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Jinglai Li
- Beijing Institute of Pharmacology and Toxicology, Beijing, People's Republic of China.
| | - Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, People's Republic of China.
| | - Fang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Hongyan Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Bosi Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| | - Jinfeng Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
- Southwest University of Science and Technology, Mianyang, People's Republic of China.
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, People's Republic of China.
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, People's Republic of China.
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18
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Sojikul P, Saithong T, Kalapanulak S, Pisuttinusart N, Limsirichaikul S, Tanaka M, Utsumi Y, Sakurai T, Seki M, Narangajavana J. Genome-wide analysis reveals phytohormone action during cassava storage root initiation. PLANT MOLECULAR BIOLOGY 2015; 88:531-43. [PMID: 26118659 DOI: 10.1007/s11103-015-0340-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/23/2015] [Indexed: 05/04/2023]
Abstract
Development of storage roots is a process associated with a phase change from cell division and elongation to radial growth and accumulation of massive amounts of reserve substances such as starch. Knowledge of the regulation of cassava storage root formation has accumulated over time; however, gene regulation during the initiation and early stage of storage root development is still poorly understood. In this study, transcription profiling of fibrous, intermediate and storage roots at eight weeks old were investigated using a 60-mer-oligo microarray. Transcription and gene expression were found to be the key regulating processes during the transition stage from fibrous to intermediate roots, while homeostasis and signal transduction influenced regulation from intermediate roots to storage roots. Clustering analysis of significant genes and transcription factors (TF) indicated that a number of phytohormone-related TF were differentially expressed; therefore, phytohormone-related genes were assembled into a network of correlative nodes. We propose a model showing the relationship between KNOX1 and phytohormones during storage root initiation. Exogeneous treatment of phytohormones N (6) -benzylaminopurine and 1-Naphthaleneacetic acid were used to induce the storage root initiation stage and to investigate expression patterns of the genes involved in storage root initiation. The results support the hypothesis that phytohormones are acting in concert to regulate the onset of cassava storage root development. Moreover, MeAGL20 is a factor that might play an important role at the onset of storage root initiation when the root tip becomes swollen.
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Affiliation(s)
- Punchapat Sojikul
- Department of Biotechnology, Center for Cassava Molecular Biotechnology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand,
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19
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Grimault A, Gendrot G, Chaignon S, Gilard F, Tcherkez G, Thévenin J, Dubreucq B, Depège-Fargeix N, Rogowsky PM. Role of B3 domain transcription factors of the AFL family in maize kernel filling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:116-25. [PMID: 26025525 DOI: 10.1016/j.plantsci.2015.03.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 05/20/2023]
Abstract
In the dicot Arabidopsis thaliana, the B3 transcription factors, ABA-INSENSITIVE 3 (ABI3), FUSCA 3 (FUS3) and LEAFY COTYLEDON 2 (LEC2) are key regulators of seed maturation. This raises the question of the role of ABI3/FUS3/LEC2 (AFL) proteins in cereals, where not only the embryo but also the persistent endosperm accumulates reserve substances. Among the five ZmAFL genes identified in the maize genome, ZmAFL2 and ZmAFL3/ZmVp1 closely resemble FUS3 and ABI3, respectively, in terms of their sequences, domain structure and gene activity profiles. Of the three genes that fall into the LEC2 phylogenetic sub-clade, ZmAFL5 and ZmAFL6 have constitutive gene activity, whereas ZmAFL4, like LEC2, has preferential gene activity in pollen and seed, although its seed gene activity is restricted to the endosperm during reserve accumulation. Knock down of ZmAFL4 gene activity perturbs carbon metabolism and reduces starch content in the developing endosperm at 20 DAP. ZmAFL4 and ZmAFL3/ZmVp1 trans-activate a maize oleosin promoter in a heterologous moss system. In conclusion our results suggest, based on gene activity profiles, that the functions of FUS3 and ABI3 could be conserved between dicot and monocot species. In contrast, LEC2 function may have partially diverged in cereals where our findings provide first evidence of the specialization of ZmAFL4 for roles in the endosperm.
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Affiliation(s)
- Aurélie Grimault
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Ghislaine Gendrot
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Sandrine Chaignon
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Françoise Gilard
- CNRS, UMR 9213, Institute of Plant Sciences Paris-Saclay, F-91405 Orsay, France
| | - Guillaume Tcherkez
- CNRS, UMR 9213, Institute of Plant Sciences Paris-Saclay, F-91405 Orsay, France
| | - Johanne Thévenin
- INRA, UMR 1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Bertrand Dubreucq
- INRA, UMR 1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France; AgroParisTech, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, Versailles, France
| | - Nathalie Depège-Fargeix
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France
| | - Peter M Rogowsky
- Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, Unité Reproduction et Développement des Plantes, F-69364 Lyon, France; INRA, UMR 879, Reproduction et Développement des Plantes, F-69364 Lyon, France; CNRS, UMR 5667, Reproduction et Développement des Plantes, F-69364 Lyon, France.
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20
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Abu-Jamous B, Fa R, Roberts DJ, Nandi AK. UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets. BMC Bioinformatics 2015; 16:184. [PMID: 26040489 PMCID: PMC4453228 DOI: 10.1186/s12859-015-0614-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/16/2015] [Indexed: 12/13/2022] Open
Abstract
Background Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently representative of real datasets. Results Here, we propose an unsupervised method for the unification of clustering results from multiple datasets using external specifications (UNCLES). This method has the ability to identify the subsets of genes consistently co-expressed in a subset of datasets while being poorly co-expressed in another subset of datasets, and to identify the subsets of genes consistently co-expressed in all given datasets. We also propose the M-N scatter plots validation technique and adopt it to set the parameters of UNCLES, such as the number of clusters, automatically. Additionally, we propose an approach for the synthesis of gene expression datasets using real data profiles in a way which combines the ground-truth-knowledge of synthetic data and the realistic expression values of real data, and therefore overcomes the problem of faithfulness of synthetic expression data modelling. By application to those datasets, we validate UNCLES while comparing it with other conventional clustering methods, and of particular relevance, biclustering methods. We further validate UNCLES by application to a set of 14 real genome-wide yeast datasets as it produces focused clusters that conform well to known biological facts. Furthermore, in-silico-based hypotheses regarding the function of a few previously unknown genes in those focused clusters are drawn. Conclusions The UNCLES method, the M-N scatter plots technique, and the expression data synthesis approach will have wide application for the comprehensive analysis of genomic and other sources of multiple complex biological datasets. Moreover, the derived in-silico-based biological hypotheses represent subjects for future functional studies. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0614-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Basel Abu-Jamous
- Department of Electronic and Computer Engineering, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK.
| | - Rui Fa
- Department of Electronic and Computer Engineering, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK.
| | - David J Roberts
- National Health Service Blood and Transplant, Oxford, OX3 9BQ, UK. .,Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | - Asoke K Nandi
- Department of Electronic and Computer Engineering, Brunel University London, Uxbridge, Middlesex, UB8 3PH, UK. .,Department of Mathematical Information Technology, University of Jyväskylä, Jyväskylä, Finland.
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21
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Alvarez Prado S, López CG, Senior ML, Borrás L. The genetic architecture of maize (Zea mays L.) kernel weight determination. G3 (BETHESDA, MD.) 2014; 4:1611-21. [PMID: 25237113 PMCID: PMC4169153 DOI: 10.1534/g3.114.013243] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/03/2014] [Indexed: 02/04/2023]
Abstract
Individual kernel weight is an important trait for maize yield determination. We have identified genomic regions controlling this trait by using the B73xMo17 population; however, the effect of genetic background on control of this complex trait and its physiological components is not yet known. The objective of this study was to understand how genetic background affected our previous results. Two nested stable recombinant inbred line populations (N209xMo17 and R18xMo17) were designed for this purpose. A total of 408 recombinant inbred lines were genotyped and phenotyped at two environments for kernel weight and five other traits related to kernel growth and development. All traits showed very high and significant (P < 0.001) phenotypic variability and medium-to-high heritability (0.60-0.90). When N209xMo17 and R18xMo17 were analyzed separately, a total of 23 environmentally stable quantitative trait loci (QTL) and five epistatic interactions were detected for N209xMo17. For R18xMo17, 59 environmentally stable QTL and 17 epistatic interactions were detected. A joint analysis detected 14 stable QTL regardless of the genetic background. Between 57 and 83% of detected QTL were population specific, denoting medium-to-high genetic background effects. This percentage was dependent on the trait. A meta-analysis including our previous B73xMo17 results identified five relevant genomic regions deserving further characterization. In summary, our grain filling traits were dominated by small additive QTL with several epistatic and few environmental interactions and medium-to-high genetic background effects. This study demonstrates that the number of detected QTL and additive effects for different physiologically related grain filling traits need to be understood relative to the specific germplasm.
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Affiliation(s)
- Santiago Alvarez Prado
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Prov. de Santa Fe, Argentina
| | - César G López
- Facultad de Ciencias Agrarias, Universidad de Lomas de Zamora, Lavallol 1836, Prov. de Buenos Aires, Argentina
| | - M Lynn Senior
- Syngenta Seeds Inc., Research Triangle Park, North Carolina 27709
| | - Lucas Borrás
- Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla S2125ZAA, Prov. de Santa Fe, Argentina
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22
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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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23
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Chen J, Zeng B, Zhang M, Xie S, Wang G, Hauck A, Lai J. Dynamic transcriptome landscape of maize embryo and endosperm development. PLANT PHYSIOLOGY 2014; 166:252-64. [PMID: 25037214 PMCID: PMC4149711 DOI: 10.1104/pp.114.240689] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues. A total of 26,105 genes were found to be involved in programming seed development, including 1,614 transcription factors. Global comparisons of gene expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with the published nonseed high-throughput RNA sequencing data, we identified 91 transcription factors and 1,167 other seed-specific genes, which should help elucidate key mechanisms and regulatory networks that underlie seed development. In addition, correlation of gene expression with the pattern of DNA methylation revealed that hypomethylation of the gene body region should be an important factor for the expressional activation of seed-specific genes, especially for extremely highly expressed genes such as zeins. This study provides a valuable resource for understanding the genetic control of seed development of monocotyledon plants.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Biao Zeng
- State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Mei Zhang
- State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Shaojun Xie
- State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Gaokui Wang
- State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Andrew Hauck
- State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Agro-biotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, People's Republic of China
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24
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Fu J, Cheng Y, Linghu J, Yang X, Kang L, Zhang Z, Zhang J, He C, Du X, Peng Z, Wang B, Zhai L, Dai C, Xu J, Wang W, Li X, Zheng J, Chen L, Luo L, Liu J, Qian X, Yan J, Wang J, Wang G. RNA sequencing reveals the complex regulatory network in the maize kernel. Nat Commun 2014; 4:2832. [PMID: 24343161 DOI: 10.1038/ncomms3832] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 10/29/2013] [Indexed: 01/19/2023] Open
Abstract
RNA sequencing can simultaneously identify exonic polymorphisms and quantitate gene expression. Here we report RNA sequencing of developing maize kernels from 368 inbred lines producing 25.8 billion reads and 3.6 million single-nucleotide polymorphisms. Both the MaizeSNP50 BeadChip and the Sequenom MassArray iPLEX platforms confirm a subset of high-quality SNPs. Of these SNPs, we have mapped 931,484 to gene regions with a mean density of 40.3 SNPs per gene. The genome-wide association study identifies 16,408 expression quantitative trait loci. A two-step approach defines 95.1% of the eQTLs to a 10-kb region, and 67.7% of them include a single gene. The establishment of relationships between eQTLs and their targets reveals a large-scale gene regulatory network, which include the regulation of 31 zein and 16 key kernel genes. These results contribute to our understanding of kernel development and to the improvement of maize yield and nutritional quality.
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Affiliation(s)
- Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Jingjing Linghu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lin Kang
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Zhang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Cheng He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhiyu Peng
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Bo Wang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lihong Zhai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Dai
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Jiabao Xu
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Weidong Wang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiangru Li
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Chen
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Longhai Luo
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Junjie Liu
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Xiaoju Qian
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Wang
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Valdés A, Ibáñez C, Simó C, García-Cañas V. Recent transcriptomics advances and emerging applications in food science. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.06.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Basnet RK, Moreno-Pachon N, Lin K, Bucher J, Visser RGF, Maliepaard C, Bonnema G. Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes. BMC Genomics 2013; 14:840. [PMID: 24289287 PMCID: PMC4046715 DOI: 10.1186/1471-2164-14-840] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/13/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed. RESULTS Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways. CONCLUSIONS This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of seed quality traits.
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Affiliation(s)
| | | | | | | | | | | | - Guusje Bonnema
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
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Alvarez CE, Saigo M, Margarit E, Andreo CS, Drincovich MF. Kinetics and functional diversity among the five members of the NADP-malic enzyme family from Zea mays, a C4 species. PHOTOSYNTHESIS RESEARCH 2013; 115:65-80. [PMID: 23649167 DOI: 10.1007/s11120-013-9839-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/25/2013] [Indexed: 05/27/2023]
Abstract
NADP-malic enzyme (NADP-ME) is involved in different metabolic pathways in several organisms due to the relevant physiological functions of the substrates and products of its reaction. In plants, it is one of the most important proteins that were recruited to fulfil key roles in C4 photosynthesis. Recent advances in genomics allowed the characterization of the complete set of NADP-ME genes from some C3 species, as Arabidopsis thaliana and Oryza sativa; however, the characterization of the complete NADP-ME family from a C4 species has not been performed yet. In this study, while taking advantage of the complete Zea mays genome sequence recently released, the characterization of the whole NADP-ME family is presented. The maize NADP-ME family is composed of five genes, two encoding plastidic NADP-MEs (ZmC4- and ZmnonC4-NADP-ME), and three cytosolic enzymes (Zmcyt1-, Zmcyt2-, and Zmcyt3-NADP-ME). The results presented clearly show that each maize NADP-ME displays particular organ distribution, response to stress stimuli, and differential biochemical properties. Phylogenetic footprinting studies performed with the NADP-MEs from several grasses, indicate that four members of the maize NADP-ME family share conserved transcription factor binding motifs with their orthologs, indicating conserved physiological functions for these genes in monocots. Based on the results obtained in this study, and considering the biochemical plasticity shown by the NADP-ME, it is discussed the relevance of the presence of a multigene family, in which each member encodes an isoform with particular biochemical properties, in the evolution of the C4 NADP-ME, improved to fulfil the requirements for an efficient C4 mechanism.
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Affiliation(s)
- Clarisa E Alvarez
- Centro de Estudios Fotosintéticos y Bioquímicos CEFOBI, Universidad Nacional de Rosario, Suipacha 531, Rosario, Argentina
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Sreenivasulu N, Wobus U. Seed-development programs: a systems biology-based comparison between dicots and monocots. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:189-217. [PMID: 23451786 DOI: 10.1146/annurev-arplant-050312-120215] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Seeds develop differently in dicots and monocots, especially with respect to the major storage organs. High-resolution transcriptome data have provided the first insights into the molecular networks and pathway interactions that function during the development of individual seed compartments. Here, we review mainly recent data obtained by systems biology-based approaches, which have allowed researchers to construct and model complex metabolic networks and fluxes and identify key limiting steps in seed development. Comparative coexpression network analyses define evolutionarily conservative (FUS3/ABI3/LEC1) and divergent (LEC2) networks in dicots and monocots. Finally, we discuss the determination of seed size--an important yield-related characteristic--as mediated by a number of processes (maternal and epigenetic factors, fine-tuned regulation of cell death in distinct seed compartments, and endosperm growth) and underlying genes defined through mutant analyses. Altogether, systems approaches can make important contributions toward a more complete and holistic knowledge of seed biology and thus support strategies for knowledge-based molecular breeding.
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Affiliation(s)
- Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.
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Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Khurana JP, Tyagi AK, Kapoor S. Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics 2012. [PMID: 22466020 DOI: 10.1007/s10142‐012‐0274‐3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.
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Affiliation(s)
- Rita Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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Barthole G, Lepiniec L, Rogowsky PM, Baud S. Controlling lipid accumulation in cereal grains. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:33-9. [PMID: 22325864 DOI: 10.1016/j.plantsci.2011.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/02/2011] [Accepted: 09/02/2011] [Indexed: 05/21/2023]
Abstract
Plant oils have so far been mostly directed toward food and feed production. Nowadays however, these oils are more and more used as competitive alternatives to mineral hydrocarbon-based products. This increasing demand for vegetable oils has led to a renewed interest in elucidating the metabolism of storage lipids and its regulation in various plant systems. Cereal grains store carbon in the form of starch in a large endosperm and as oil in an embryo of limited size. Complementary studies on kernel development and metabolism have paved the way for breeding or engineering new varieties with higher grain oil content. This could be achieved either by increasing the relative proportion of the oil-rich embryo within the grain, or by enhancing oil synthesis and accumulation in embryonic structures. For instance, diacylglycerol acyltransferase (DGAT) that catalyses the ultimate reaction in the biosynthesis of triacylglycerol appears to be a promising target for increasing oil content in maize embryos. Similarly, over-expression of the maize transcriptional regulators ZmLEAFY COTYLEDON1 and ZmWRINKLED1 efficiently stimulates oil accumulation in the kernels of transgenic lines. Redirecting carbon from starch to oil in the endosperm, though not yet realized, is discussed.
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Affiliation(s)
- Guillaume Barthole
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Route de Saint-Cyr, F-78026 Versailles, France.
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31
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Sharma R, Agarwal P, Ray S, Deveshwar P, Sharma P, Sharma N, Nijhawan A, Jain M, Singh AK, Singh VP, Khurana JP, Tyagi AK, Kapoor S. Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics 2012; 12:229-48. [PMID: 22466020 DOI: 10.1007/s10142-012-0274-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 03/02/2012] [Accepted: 03/06/2012] [Indexed: 12/20/2022]
Abstract
Carefully analyzed expression profiles can serve as a valuable reference for deciphering gene functions. We exploited the potential of whole genome microarrays to measure the spatial and temporal expression profiles of rice genes in 19 stages of vegetative and reproductive development. We could verify expression of 22,980 genes in at least one of the tissues. Differential expression analysis with respect to five vegetative tissues and preceding stages of development revealed reproductive stage-preferential/-specific genes. By using subtractive logic, we identified 354 and 456 genes expressing specifically during panicle and seed development, respectively. The metabolic/hormonal pathways and transcription factor families playing key role in reproductive development were elucidated after overlaying the expression data on the public databases and manually curated list of transcription factors, respectively. During floral meristem differentiation (P1) and male meiosis (P3), the genes involved in jasmonic acid and phenylpropanoid biosynthesis were significantly upregulated. P6 stage of panicle, containing mature gametophytes, exhibited enrichment of transcripts involved in homogalacturonon degradation. Genes regulating auxin biosynthesis were induced during early seed development. We validated the stage-specificity of regulatory regions of three panicle-specific genes, OsAGO3, OsSub42, and RTS, and an early seed-specific gene, XYH, in transgenic rice. The data generated here provides a snapshot of the underlying complexity of the gene networks regulating rice reproductive development.
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Affiliation(s)
- Rita Sharma
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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32
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Capron D, Mouzeyar S, Boulaflous A, Girousse C, Rustenholz C, Laugier C, Paux E, Bouzidi MF. Transcriptional profile analysis of E3 ligase and hormone-related genes expressed during wheat grain development. BMC PLANT BIOLOGY 2012; 12:35. [PMID: 22416807 PMCID: PMC3405487 DOI: 10.1186/1471-2229-12-35] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 03/14/2012] [Indexed: 05/23/2023]
Abstract
BACKGROUND Wheat grains are an important source of food, stock feed and raw materials for industry, but current production levels cannot meet world needs. Elucidation of the molecular mechanisms underlying wheat grain development will contribute valuable information to improving wheat cultivation. One of the most important mechanisms implicated in plant developmental processes is the ubiquitin-proteasome system (UPS). Among the different roles of the UPS, it is clear that it is essential to hormone signaling. In particular, E3 ubiquitin ligases of the UPS have been shown to play critical roles in hormone perception and signal transduction. RESULTS A NimbleGen microarray containing 39,179 UniGenes was used to study the kinetics of gene expression during wheat grain development from the early stages of cell division to the mid-grain filling stage. By comparing 11 consecutive time-points, 9284 differentially expressed genes were identified and annotated during this study. A comparison of the temporal profiles of these genes revealed dynamic transcript accumulation profiles with major reprogramming events that occurred during the time intervals of 80-120 and 220-240°Cdays. The list of the genes expressed differentially during these transitions were identified and annotated. Emphasis was placed on E3 ligase and hormone-related genes. In total, 173 E3 ligase coding genes and 126 hormone-related genes were differentially expressed during the cell division and grain filling stages, with each family displaying a different expression profile. CONCLUSIONS The differential expression of genes involved in the UPS and plant hormone pathways suggests that phytohormones and UPS crosstalk might play a critical role in the wheat grain developmental process. Some E3 ligase and hormone-related genes seem to be up- or down-regulated during the early and late stages of the grain development.
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Affiliation(s)
- Delphine Capron
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
| | - Said Mouzeyar
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
| | - Aurélia Boulaflous
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
| | - Christine Girousse
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Camille Rustenholz
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Christel Laugier
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Etienne Paux
- INRA, UMR 1095 GDEC, 234 avenue du Brézet, F-63100 Clermont-Ferrand, France
| | - Mohamed Fouad Bouzidi
- Université Blaise Pascal, UMR 1095 GDEC, 24 avenue des Landais, F-63177 Aubière, France
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Xue LJ, Zhang JJ, Xue HW. Genome-wide analysis of the complex transcriptional networks of rice developing seeds. PLoS One 2012; 7:e31081. [PMID: 22363552 PMCID: PMC3281924 DOI: 10.1371/journal.pone.0031081] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 01/02/2012] [Indexed: 11/18/2022] Open
Abstract
Background The development of rice (Oryza sativa) seed is closely associated with assimilates storage and plant yield, and is fine controlled by complex regulatory networks. Exhaustive transcriptome analysis of developing rice embryo and endosperm will help to characterize the genes possibly involved in the regulation of seed development and provide clues of yield and quality improvement. Principal Findings Our analysis showed that genes involved in metabolism regulation, hormone response and cellular organization processes are predominantly expressed during rice development. Interestingly, 191 transcription factor (TF)-encoding genes are predominantly expressed in seed and 59 TFs are regulated during seed development, some of which are homologs of seed-specific TFs or regulators of Arabidopsis seed development. Gene co-expression network analysis showed these TFs associated with multiple cellular and metabolism pathways, indicating a complex regulation of rice seed development. Further, by employing a cold-resistant cultivar Hanfeng (HF), genome-wide analyses of seed transcriptome at normal and low temperature reveal that rice seed is sensitive to low temperature at early stage and many genes associated with seed development are down-regulated by low temperature, indicating that the delayed development of rice seed by low temperature is mainly caused by the inhibition of the development-related genes. The transcriptional response of seed and seedling to low temperature is different, and the differential expressions of genes in signaling and metabolism pathways may contribute to the chilling tolerance of HF during seed development. Conclusions These results provide informative clues and will significantly improve the understanding of rice seed development regulation and the mechanism of cold response in rice seed.
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Affiliation(s)
- Liang-Jiao Xue
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing-Jing Zhang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Wei Xue
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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Xiao L, Wang H, Wan P, Kuang T, He Y. Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens. BMC PLANT BIOLOGY 2011; 11:177. [PMID: 22168156 PMCID: PMC3264550 DOI: 10.1186/1471-2229-11-177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 12/15/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND Regulation of gene expression plays a pivotal role in controlling the development of multicellular plants. To explore the molecular mechanism of plant developmental-stage transition and cell-fate determination, a genome-wide analysis was undertaken of sequential developmental time-points and individual tissue types in the model moss Physcomitrella patens because of the short life cycle and relative structural simplicity of this plant. RESULTS Gene expression was analyzed by digital gene expression tag profiling of samples taken from P. patens protonema at 3, 14 and 24 days, and from leafy shoot tissues at 30 days, after protoplast isolation, and from 14-day-old caulonemal and chloronemal tissues. In total, 4333 genes were identified as differentially displayed. Among these genes, 4129 were developmental-stage specific and 423 were preferentially expressed in either chloronemal or caulonemal tissues. Most of the differentially displayed genes were assigned to functions in organic substance and energy metabolism or macromolecule biosynthetic and catabolic processes based on gene ontology descriptions. In addition, some regulatory genes identified as candidates might be involved in controlling the developmental-stage transition and cell differentiation, namely MYB-like, HB-8, AL3, zinc finger family proteins, bHLH superfamily, GATA superfamily, GATA and bZIP transcription factors, protein kinases, genes related to protein/amino acid methylation, and auxin, ethylene, and cytokinin signaling pathways. CONCLUSIONS These genes that show highly dynamic changes in expression during development in P. patens are potential targets for further functional characterization and evolutionary developmental biology studies.
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Affiliation(s)
- Lihong Xiao
- College of Life Science, Capital Normal University, Beijing, 100048, P. R. China
| | - Hui Wang
- College of Life Science, Capital Normal University, Beijing, 100048, P. R. China
| | - Ping Wan
- College of Life Science, Capital Normal University, Beijing, 100048, P. R. China
| | - Tingyun Kuang
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P. R. China
| | - Yikun He
- College of Life Science, Capital Normal University, Beijing, 100048, P. R. China
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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: 28] [Impact Index Per Article: 2.2] [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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Jamil A, Riaz S, Ashraf M, Foolad MR. Gene Expression Profiling of Plants under Salt Stress. CRITICAL REVIEWS IN PLANT SCIENCES 2011; 30:435-458. [PMID: 0 DOI: 10.1080/07352689.2011.605739] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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37
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Liu YY, Li JZ, Li YL, Wei MG, Cui QX, Wang QL. Identification of differentially expressed genes at two key endosperm development stages using two maize inbreds with large and small grain and integration with detected QTL for grain weight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:433-47. [PMID: 20364377 DOI: 10.1007/s00122-010-1321-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Accepted: 03/05/2010] [Indexed: 05/24/2023]
Abstract
Maize endosperm accounts for more than 80% of the grain weight. Cell division and grain filling are the two key stages for endosperm development. Previous studies showed that gene expression during differential stages in endosperm development is greatly different. However, information on systematic identification and characterization of the differentially expressed genes between the two stages are limited. In this study, suppression subtractive hybridization (SSH) was used to generate four subtracted cDNA libraries for the two stages using two maize inbreds with large and small grain. Totally, 4,784 differentially expressed sequence tags (ESTs) were sequenced and 902 were non-redundant, which consisted of 344 unique ESTs. Among them 192 had high sequence similarity to the GenBank entries and represent diverse of functional categories, such as metabolism, cell growth/division, transcription, signal transduction, protein destination/storage, protein synthesis and others. The expression patterns of 75.7% SSH-derived cDNAs were confirmed by reverse Northern blot and semi-quantitative reverse transcription polymerase chain reaction, and exhibited the similar results (75.0%). Genes differentially expressed between two key stages for the two inbreds were involved in diverse physiological process pathway, which might be responsible for the formation of grain weight. 43.8% (70 of the 160 unique ESTs) of the identified ESTs were assigned to 39 chromosome bins distributed over all ten maize chromosomes. Eleven ESTs were found to co-localize with previous detected QTLs for grain weight, which might be considered as the candidate genes of grain weight for further study.
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Affiliation(s)
- Y Y Liu
- College of Agriculture, Henan Agricultural University, 95 Wenhua Rd, Zhengzhou, China
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Wang G, Wang H, Zhu J, Zhang J, Zhang X, Wang F, Tang Y, Mei B, Xu Z, Song R. An expression analysis of 57 transcription factors derived from ESTs of developing seeds in Maize (Zea mays). PLANT CELL REPORTS 2010; 29:545-59. [PMID: 20336461 DOI: 10.1007/s00299-010-0843-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 03/05/2010] [Accepted: 03/08/2010] [Indexed: 05/19/2023]
Abstract
Maize seeds are an important source of food, animal feed, and industrial raw materials. To understand global gene expression and regulation during maize seed development, a normalized cDNA library, covering most of the developmental stages of maize seeds, was constructed. Sequencing analysis of 10,848 randomly selected clones identified 6,630 unique ESTs. Among them, 57 putative transcription factors (TFs) were identified. The TFs belong to seven different super-families, specifically 17 Zinc-finger, 13 bZIP, 8 bHLH, 6 MADS, 7 MYB, 3 Homedomain, and 3 AP2/EREBP. The spatial and temporal expression of the TFs was analyzed by semi-quantitative RT-PCR with representative tissue types and seeds at different developmental stages, revealing their diverse expression patterns and expression levels. One-third (19) of the maize TFs was found their putative orthologs in Arabidopsis. Similar expression patterns were observed in both maize and Arabidopsis for the majority of orthologous pairs (15 out of 19), suggesting their conserved functions during seed development. In conclusion, the systematic analysis of maize seed TFs has provided valuable insight into transcriptional regulation during maize seed development.
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Affiliation(s)
- Guifeng Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, No. 333 Nanchen Road, Shanghai, People's Republic of China
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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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Jones SI, Gonzalez DO, Vodkin LO. Flux of transcript patterns during soybean seed development. BMC Genomics 2010; 11:136. [PMID: 20181280 PMCID: PMC2846912 DOI: 10.1186/1471-2164-11-136] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 02/24/2010] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consisting of up to 27,000 soybean cDNAs. A subset of these genes on a highly-repetitive 70-mer oligonucleotide microarray was also used to support the results. RESULTS It was discovered that genes related to cell growth and maintenance processes, as well as energy processes like photosynthesis, decreased in expression levels as the cotyledons approached the mature, dry stage. Genes involved with some storage proteins had their highest expression levels at the stage of highest fresh weight. However, genes encoding many transcription factors and DNA binding proteins showed higher expression levels in the desiccating and dry seeds than in most of the green stages. CONCLUSIONS Data on 27,000 cDNAs have been obtained over five stages of soybean development, including the stages of major accumulation of agronomically-important products, using two different types of microarrays. Of particular interest are the genes found to peak in expression at the desiccating and dry seed stages, such as those annotated as transcription factors, which may indicate the preparation of pathways that will be needed later in the early stages of imbibition and germination.
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Affiliation(s)
- Sarah I Jones
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Delkin O Gonzalez
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
- Current address: Dow AgroSciences, Indianaoplis, IN 46268, USA
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
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The contribution of cell cycle regulation to endosperm development. ACTA ACUST UNITED AC 2009; 22:207-19. [DOI: 10.1007/s00497-009-0105-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 07/05/2009] [Indexed: 01/08/2023]
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Manicacci D, Camus-Kulandaivelu L, Fourmann M, Arar C, Barrault S, Rousselet A, Feminias N, Consoli L, Francès L, Méchin V, Murigneux A, Prioul JL, Charcosset A, Damerval C. Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize. PLANT PHYSIOLOGY 2009; 150:506-20. [PMID: 19329568 PMCID: PMC2675748 DOI: 10.1104/pp.108.131888] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 03/23/2009] [Indexed: 05/18/2023]
Abstract
Association genetics is a powerful method to track gene polymorphisms responsible for phenotypic variation, since it takes advantage of existing collections and historical recombination to study the correlation between large genetic diversity and phenotypic variation. We used a collection of 375 maize (Zea mays ssp. mays) inbred lines representative of tropical, American, and European diversity, previously characterized for genome-wide neutral markers and population structure, to investigate the roles of two functionally related candidate genes, Opaque2 and CyPPDK1, on kernel quality traits. Opaque2 encodes a basic leucine zipper transcriptional activator specifically expressed during endosperm development that controls the transcription of many target genes, including CyPPDK1, which encodes a cytosolic pyruvate orthophosphate dikinase. Using statistical models that correct for population structure and individual kinship, Opaque2 polymorphism was found to be strongly associated with variation of the essential amino acid lysine. This effect could be due to the direct role of Opaque2 on either zein transcription, zeins being major storage proteins devoid of lysine, or lysine degradation through the activation of lysine ketoglutarate reductase. Moreover, we found that a polymorphism in the Opaque2 coding sequence and several polymorphisms in the CyPPDK1 promoter nonadditively interact to modify both lysine content and the protein-versus-starch balance, thus revealing the role in quantitative variation in plants of epistatic interactions between a transcriptional activator and one of its target genes.
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Affiliation(s)
- Domenica Manicacci
- University Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif sur Yvette, France.
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