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Das AK, Hao L. Functional characterization of ZmbHLH121, a bHLH transcription factor, focusing on Zea mays kernel development. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Liu X, Yue Y, Gu Z, Huang Q, Pan Z, Zhao Z, Zheng M, Zhang Z, Li C, Yi H, Yu T, Cao M. The characterization and candidate gene isolation for a novel male-sterile mutant ms40 in maize. PLANT CELL REPORTS 2021; 40:1957-1970. [PMID: 34319484 DOI: 10.1007/s00299-021-02762-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
A novel genic male-sterile mutant ms40 was obtained from EMS treated RP125. The key candidate gene ZmbHLH51 located on chromosome 4 was identified by map-based cloning. This study further enriched the male sterile gene resources for both production applications and theoretical studies of abortion mechanisms. Maize male-sterile mutant 40 (ms40) was obtained from the progeny of the ethyl methanesulfonate (EMS) treated inbred line RP125. Genetic analysis indicated that the sterility was controlled by a single recessive nuclear gene. Cytological observation of anthers revealed that the cuticles of ms40 anthers were abnormal, and no Ubisch bodies were observed on the inner surface of ms40 anthers through scanning electron microscopy(SEM). Moreover, its tapetum exhibited delayed degradation and then blocked the formation of normal microspores. Using map-based cloning strategy, the ms40 locus was found to locate in a 282-kb interval on chromosome 4, and five annotated genes were predicted within this region. PCR-based sequencing detected a single non-synonymous SNP (G > A) that changed glycine (G) to arginine (A) in the seventh exon of Zm00001d053895, while no sequence difference between ms40 and RP125 was found for the other four genes. Zm00001d053895 encodes the bHLH transcription factor ZmbHLH51 which is localized in the nucleus. Phylogenetic analysis showed that ZmbHLH51 had the highest homology with Sb04g001650, a tapetum degeneration retardation (TDR) bHLH transcription factor in Sorghum bicolor. Co-expression analysis revealed a total of 1192 genes co-expressed with ZmbHLH51 in maize, 647 of which were anther-specific genes. qRT-PCR results suggested the expression levels of some known genes related to anther development were affected in ms40. In summary, these findings revealed the abortion characteristics of ms40 anthers and lay a foundation for further studies on the mechanisms of male fertility.
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Affiliation(s)
- Xiaowei Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yujing Yue
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zicheng Gu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Qiang Huang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- Sichuan Institute of Atomic Energy, Chengdu, China
| | - Zijin Pan
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zhuofan Zhao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mingmin Zheng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, China
| | - Zhiming Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Chuan Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hongyang Yi
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Tao Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China.
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Zhang F, Wu J, Sade N, Wu S, Egbaria A, Fernie AR, Yan J, Qin F, Chen W, Brotman Y, Dai M. Genomic basis underlying the metabolome-mediated drought adaptation of maize. Genome Biol 2021; 22:260. [PMID: 34488839 PMCID: PMC8420056 DOI: 10.1186/s13059-021-02481-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive. Results Here, we perform non-targeted metabolic profiling of leaves for 385 maize natural inbred lines grown under well-watered as well as drought-stressed conditions. A total of 3890 metabolites are identified and 1035 of these are differentially produced between well-watered and drought-stressed conditions, representing effective indicators of maize drought response and tolerance. Genetic dissections reveal the associations between these metabolites and thousands of single-nucleotide polymorphisms (SNPs), which represented 3415 metabolite quantitative trait loci (mQTLs) and 2589 candidate genes. 78.6% of mQTLs (2684/3415) are novel drought-responsive QTLs. The regulatory variants that control the expression of the candidate genes are revealed by expression QTL (eQTL) analysis of the transcriptomes of leaves from 197 maize natural inbred lines. Integrated metabolic and transcriptomic assays identify dozens of environment-specific hub genes and their gene-metabolite regulatory networks. Comprehensive genetic and molecular studies reveal the roles and mechanisms of two hub genes, Bx12 and ZmGLK44, in regulating maize metabolite biosynthesis and drought tolerance. Conclusion Our studies reveal the first population-level metabolomes in crop drought response and uncover the natural variations and genetic control of these metabolomes underlying crop drought adaptation, demonstrating that multi-omics is a powerful strategy to dissect the genetic mechanisms of crop complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02481-1.
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Affiliation(s)
- Fei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Jinfeng Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Nir Sade
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aiman Egbaria
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany. .,Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Beersheba, Israel.
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan laboratory, Wuhan, 430070, China.
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Jiang Y, An X, Li Z, Yan T, Zhu T, Xie K, Liu S, Hou Q, Zhao L, Wu S, Liu X, Zhang S, He W, Li F, Li J, Wan X. CRISPR/Cas9-based discovery of maize transcription factors regulating male sterility and their functional conservation in plants. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1769-1784. [PMID: 33772993 PMCID: PMC8428822 DOI: 10.1111/pbi.13590] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 05/12/2023]
Abstract
Identifying genic male-sterility (GMS) genes and elucidating their roles are important to unveil plant male reproduction and promote their application in crop breeding. However, compared with Arabidopsis and rice, relatively fewer maize GMS genes have been discovered and little is known about their regulatory pathways underlying anther and pollen development. Here, by sequencing and analysing anther transcriptomes at 11 developmental stages in maize B73, Zheng58 and M6007 inbred lines, 1100 transcription factor (TF) genes were identified to be stably differentially expressed among different developmental stages. Among them, 14 maize TF genes (9 types belonging to five TF families) were selected and performed CRISPR/Cas9-mediated gene mutagenesis, and then, 12 genes in eight types, including ZmbHLH51, ZmbHLH122, ZmTGA9-1/-2/-3, ZmTGA10, ZmMYB84, ZmMYB33-1/-2, ZmPHD11 and ZmLBD10/27, were identified as maize new GMS genes by using DNA sequencing, phenotypic and cytological analyses. Notably, ZmTGA9-1/-2/-3 triple-gene mutants and ZmMYB33-1/-2 double-gene mutants displayed complete male sterility, but their double- or single-gene mutants showed male fertility. Similarly, ZmLBD10/27 double-gene mutant displayed partial male sterility with 32.18% of aborted pollen grains. In addition, ZmbHLH51 was transcriptionally activated by ZmbHLH122 and their proteins were physically interacted. Molecular markers co-segregating with these GMS mutations were developed to facilitate their application in maize breeding. Finally, all 14-type maize GMS TF genes identified here and reported previously were compared on functional conservation and diversification among maize, rice and Arabidopsis. These findings enrich GMS gene and mutant resources for deeply understanding the regulatory network underlying male fertility and for creating male-sterility lines in maize.
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Affiliation(s)
- Yilin Jiang
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Xueli An
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Ziwen Li
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Tingwei Yan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Taotao Zhu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Ke Xie
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Shuangshuang Liu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Quancan Hou
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Lina Zhao
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Suowei Wu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Xinze Liu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Shaowei Zhang
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Wei He
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Fan Li
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
| | - Jinping Li
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center of USTBUniversity of Science and Technology Beijing (USTB)BeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech BreedingBeijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. LtdBeijingChina
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Jaqueth JS, Hou Z, Zheng P, Ren R, Nagel BA, Cutter G, Niu X, Vollbrecht E, Greene TW, Kumpatla SP. Fertility restoration of maize CMS-C altered by a single amino acid substitution within the Rf4 bHLH transcription factor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:101-111. [PMID: 31487408 DOI: 10.1111/tpj.14521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 05/24/2023]
Abstract
Type C cytoplasmic male sterility (CMS-C) is the most commonly used form of CMS in maize hybrid seed production. Restorer of fertility 4 (Rf4), the major fertility restorer gene of CMS-C, is located on chromosome 8S. To positionally clone Rf4, a large F3 population derived from a cross between a non-restorer and restorer (n = 5104) was screened for recombinants and then phenotyped for tassel fertility, resulting in a final map-based cloning interval of 12 kb. Within this 12-kb interval, the only likely candidate for Rf4 was GRMZM2G021276, a basic helix-loop-helix (bHLH) transcription factor with tassel-specific expression. The Rf4 gene product contains a nuclear localization signal and is likely to not interact directly with the mitochondria. Sequence analysis of Rf4 revealed four encoded amino acid substitutions between restoring and non-restoring inbreds, however only one substitution, F187Y, was within the highly conserved bHLH domain. The hypothesis that Rf4 restoration is altered by a single amino acid was tested by using clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated protein 9 (Cas9) homology directed repair (HDR) to create isogenic lines that varied for the F187Y substitution. In a population of these CRISPR-Cas9 edited plants (n = 780) that was phenotyped for tassel fertility, plants containing F187 were completely fertile, indicating fertility restoration, and plants containing Y187 were sterile, indicating lack of fertility restoration. Structural modeling shows that this amino acid residue 187 is located within the four helix bundle core, a critical region for stabilizing dimer conformation and affecting interaction partner selection.
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Affiliation(s)
| | - Zhenglin Hou
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Peizhong Zheng
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Ruihua Ren
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Bruce A Nagel
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Gary Cutter
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Xiaomu Niu
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Erik Vollbrecht
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Thomas W Greene
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Siva P Kumpatla
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
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6
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Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Proc Natl Acad Sci U S A 2019; 116:3091-3099. [PMID: 30718437 DOI: 10.1073/pnas.1817621116] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under light-dark cycles and under total darkness and obtained eight time-ordered gene coexpression networks (TO-GCNs), which can be used to predict upstream regulators of any genes in the GCNs. One of the eight TO-GCNs is light-independent and likely includes all genes involved in the development of Kranz anatomy, which is a structure crucial for the high efficiency of photosynthesis in C4 plants. Using this TO-GCN, we predicted and experimentally validated a regulatory cascade upstream of SHORTROOT1, a key Kranz anatomy regulator. Moreover, we applied the method to compare transcriptomes from maize and rice leaf segments and identified regulators of maize C4 enzyme genes and RUBISCO SMALL SUBUNIT2 Our study provides not only a powerful method but also novel insights into the regulatory networks underlying Kranz anatomy development and C4 photosynthesis.
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7
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Zhao L, Liu A, Song T, Jin Y, Xu X, Gao Y, Ye X, Qi H. Transcriptome analysis reveals the effects of grafting on sugar and α-linolenic acid metabolisms in fruits of cucumber with two different rootstocks. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:289-302. [PMID: 30036858 DOI: 10.1016/j.plaphy.2018.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 05/22/2023]
Abstract
Flavor quality in cucumber is affected by different rootstocks, but the molecular mechanism is largely unclean. To clarify the differences of sugar and aromatic compounds, cucumber (cucumis sativus) fruits from plants of self-grafted (SG) or grafted onto figleaf gourd (Cucurbita ficifolia; G1) or 'Weisheng No.1' rootstock (Cucurbita moschata ⅹCucurbita moschata hybrids; G2) were performed the transcriptome analysis. We obtained 1013 and 920 differentially expressed genes (DEGs) from G1 and G2 compared to SG respectively, in which 453 genes were co-expressed. Functional annotations showed many DEGs were involved in glycolysis/gluconeogenesis metabolism, fructose metabolism and α-Linolenic acid metabolisms, 20 DEGs were selected from the 3 pathways to validate sequencing accuracy by quantitative real-time PCR. The gene relative expression levels were concurrent with RNA-seq results and sugar and aromatic compounds content phenotypes. Moreover, some vital transcript factors and transport proteins were analyzed. These findings indicate that different rootstocks could induce significantly changes in the physiological profiling and transcripts of sugar- and aromatic flavor-related genes. This study provides a novel insight into the molecular mechanisms of fruit quality regulated by candidate genes.
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Affiliation(s)
- Lili Zhao
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China; Institute of Vegetable Research, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110866, China.
| | - Aiqun Liu
- Institute of Vegetable Research, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110866, China.
| | - Tiefeng Song
- Institute of Vegetable Research, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning 110866, China.
| | - Yazhong Jin
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilong Jiang 163319, China.
| | - Xin Xu
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China.
| | - Yang Gao
- Agricultural Technology Extension Centre of Changtu' Country, Tieling, Liaoning 112599, China.
| | - Xueling Ye
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China.
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National& Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology(Liaoning), Shenyang 110866, China.
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8
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Predicting Transcription Factor Binding Sites and Their Cognate Transcription Factors Using Gene Expression Data. Methods Mol Biol 2018. [PMID: 28623591 DOI: 10.1007/978-1-4939-7125-1_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A transcription factor (TF) is a DNA binding protein that targets specific binding-sites (TFBSs) to regulate the transcript levels of its downstream genes. Thus, identifying the TF-TFBS pairs is a pivotal step in understanding the function of TFs and the regulatory network in an organism. Here, we describe two methods for predicting the TFBS of a given TF and for predicting the cognate TF of a given TFBS from a set of strongly co-expressed genes, using time-course transcriptome data of maize developing leaves.
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Sharma A, Wai CM, Ming R, Yu Q. Diurnal Cycling Transcription Factors of Pineapple Revealed by Genome-Wide Annotation and Global Transcriptomic Analysis. Genome Biol Evol 2017; 9:2170-2190. [PMID: 28922793 PMCID: PMC5737478 DOI: 10.1093/gbe/evx161] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/22/2022] Open
Abstract
Circadian clock provides fitness advantage by coordinating internal metabolic and physiological processes to external cyclic environments. Core clock components exhibit daily rhythmic changes in gene expression, and the majority of them are transcription factors (TFs) and transcription coregulators (TCs). We annotated 1,398 TFs from 67 TF families and 80 TCs from 20 TC families in pineapple, and analyzed their tissue-specific and diurnal expression patterns. Approximately 42% of TFs and 45% of TCs displayed diel rhythmic expression, including 177 TF/TCs cycling only in the nonphotosynthetic leaf tissue, 247 cycling only in the photosynthetic leaf tissue, and 201 cycling in both. We identified 68 TF/TCs whose cycling expression was tightly coupled between the photosynthetic and nonphotosynthetic leaf tissues. These TF/TCs likely coordinate key biological processes in pineapple as we demonstrated that this group is enriched in homologous genes that form the core circadian clock in Arabidopsis and includes a STOP1 homolog. Two lines of evidence support the important role of the STOP1 homolog in regulating CAM photosynthesis in pineapple. First, STOP1 responds to acidic pH and regulates a malate channel in multiple plant species. Second, the cycling expression pattern of the pineapple STOP1 and the diurnal pattern of malate accumulation in pineapple leaf are correlated. We further examined duplicate-gene retention and loss in major known circadian genes and refined their evolutionary relationships between pineapple and other plants. Significant variations in duplicate-gene retention and loss were observed for most clock genes in both monocots and dicots.
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Affiliation(s)
- Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
- Department of Plant Pathology and Microbiology, Texas A&M University
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10
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Zhu Q, Gao P, Liu S, Zhu Z, Amanullah S, Davis AR, Luan F. Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening. BMC Genomics 2017; 18:3. [PMID: 28049426 PMCID: PMC5209866 DOI: 10.1186/s12864-016-3442-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/19/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important crop with an attractive ripe fruit that has colorful flesh. Fruit ripening is a complex, genetically programmed process. RESULTS In this study, a comparative transcriptome analysis was performed to identify the regulators and pathways that are involved in the fruit ripening of pale-yellow-flesh cultivated watermelon (COS) and red-flesh cultivated watermelon (LSW177). We first identified 797 novel genes to extend the available reference gene set. Second, 3958 genes in COS and 3503 genes in LSW177 showed at least two-fold variation in expression, and a large number of these differentially expressed genes (DEGs) during fruit ripening were related to carotenoid biosynthesis, plant hormone pathways, and sugar and cell wall metabolism. Third, we noted a correlation between ripening-associated transcripts and metabolites and the key function of these metabolic pathways during fruit ripening. CONCLUSION The results revealed several ripening-associated actions and provide novel insights into the molecular mechanisms underlying the regulation of watermelon fruit ripening.
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Affiliation(s)
- Qianglong Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Sikandar Amanullah
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Angela R Davis
- South Central Agricultural Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Currently with HM. Clause 9241 Mace Blvd, Davis, CA, 95618, USA
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China.
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China.
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11
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Nan GL, Zhai J, Arikit S, Morrow D, Fernandes J, Mai L, Nguyen N, Meyers BC, Walbot V. MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize. Development 2016; 144:163-172. [PMID: 27913638 DOI: 10.1242/dev.140673] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/21/2016] [Indexed: 11/20/2022]
Abstract
Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed. Microarray transcript profiling demonstrates a more severe developmental disruption in ms23-ref than in ms32 anthers, which possess a different bHLH defect. RNA-seq and proteomics data together with yeast two-hybrid assays suggest that MS23 along with MS32, bHLH122 and bHLH51 act sequentially as either homo- or heterodimers to choreograph tapetal development. Among them, MS23 is the earliest-acting factor, upstream of bHLH51 and bHLH122, controlling tapetal specification and maturation. By contrast, MS32 is constitutive and independently regulated and is required later than MS23 in tapetal differentiation.
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Affiliation(s)
- Guo-Ling Nan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jixian Zhai
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA.,Department of Biology, South University of Science and Technology, Shenzhen 518055, China
| | - Siwaret Arikit
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Darren Morrow
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - John Fernandes
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Lan Mai
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nhi Nguyen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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12
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Tsai KJ, Lu MYJ, Yang KJ, Li M, Teng Y, Chen S, Ku MSB, Li WH. Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance. Sci Rep 2016; 6:35076. [PMID: 27734962 PMCID: PMC5062080 DOI: 10.1038/srep35076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/23/2016] [Indexed: 12/23/2022] Open
Abstract
The diploid C4 plant foxtail millet (Setaria italica L. Beauv.) is an important crop in many parts of Africa and Asia for the vast consumption of its grain and ability to grow in harsh environments, but remains understudied in terms of complete genomic architecture. To date, there have been only two genome assembly and annotation efforts with neither assembly reaching over 86% of the estimated genome size. We have combined de novo assembly with custom reference-guided improvements on a popular cultivar of foxtail millet and have achieved a genome assembly of 477 Mbp in length, which represents over 97% of the estimated 490 Mbp. The assembly anchors over 98% of the predicted genes to the nine assembled nuclear chromosomes and contains more functional annotation gene models than previous assemblies. Our annotation has identified a large number of unique gene ontology terms related to metabolic activities, a region of chromosome 9 with several growth factor proteins, and regions syntenic with pearl millet or maize genomic regions that have been previously shown to affect growth. The new assembly and annotation for this important species can be used for detailed investigation and future innovations in growth for millet and other grains.
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Affiliation(s)
- Kevin J. Tsai
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11574 Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, 11221 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Kai-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Mengyun Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Yuchuan Teng
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Shihmay Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
| | - Maurice S. B. Ku
- Department of Bioagricultural Science, National Chiayi University, Chiayi, 60004 Taiwan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11574 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
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13
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Wang Y, Lu W, Deng D. Bioinformatic landscapes for plant transcription factor system research. PLANTA 2016; 243:297-304. [PMID: 26719053 DOI: 10.1007/s00425-015-2453-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/16/2015] [Indexed: 06/05/2023]
Abstract
Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants. Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.
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Affiliation(s)
- Yijun Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
| | - Wenjie Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Dexiang Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
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14
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Burgess SJ, Hibberd JM. Insights into C4 metabolism from comparative deep sequencing. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:138-144. [PMID: 26051034 DOI: 10.1016/j.pbi.2015.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 05/06/2015] [Accepted: 05/16/2015] [Indexed: 06/04/2023]
Abstract
C4 photosynthesis suppresses the oxygenation activity of Ribulose Bisphosphate Carboxylase Oxygenase and so limits photorespiration. Although highly complex, it is estimated to have evolved in 66 plant lineages, with the vast majority lacking sequenced genomes. Transcriptomics has recently initiated assessments of the degree to which transcript abundance differs between C3 and C4 leaves, identified novel components of C4 metabolism, and also led to mathematical models explaining the repeated evolution of this complex phenotype. Evidence is accumulating that this complex and convergent phenotype is partly underpinned by parallel evolution of structural genes, but also regulatory elements in both cis and trans. Furthermore, it appears that initial events associated with acquisition of C4 traits likely represent evolutionary exaptations related to non-photosynthetic processes.
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Affiliation(s)
- Steven J Burgess
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
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15
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Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors. Proc Natl Acad Sci U S A 2015; 112:E2477-86. [PMID: 25918418 DOI: 10.1073/pnas.1500605112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up- and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development.
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