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Wang Y, Bi Y, Jiang F, Shaw RK, Sun J, Hu C, Guo R, Fan X. Mapping and Functional Analysis of QTL for Kernel Number per Row in Tropical and Temperate-Tropical Introgression Lines of Maize ( Zea mays L.). Curr Issues Mol Biol 2023; 45:4416-4430. [PMID: 37232750 DOI: 10.3390/cimb45050281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F7 recombinant inbred line (RIL) populations were created using a temperate-tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids.
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Affiliation(s)
- Yuling Wang
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Ranjan Kumar Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jiachen Sun
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650500, China
| | - Can Hu
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
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Sun Y, Zhu Y, Cheng P, Zhang M, Wang N, Cui Z, Wei M, Xu W. A Z-Linked E3 Ubiquitin Ligase Cs-rchy1 Is Involved in Gametogenesis in Chinese Tongue Sole, Cynoglossus semilaevis. Animals (Basel) 2021; 11:ani11113265. [PMID: 34827998 PMCID: PMC8614299 DOI: 10.3390/ani11113265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The sexual growth dimorphism prevails in animals and this phenomenon is even more obvious in marine fish, so understanding the mechanism of gonadal development and gametogenesis is of great importance for sex control, thus increased productivity in aquaculture. In mammal, ubiquitin ligase plays a versatile role in gonadal development and spermatogenesis, whereas its function in fish is little reported. Using Cynoglossus semilaevis (one-year-old female individual usually grows 2–4 times bigger than male) as the fish model, a Z-chromosome linked ubiquitin ligase neurl3 was previously identified and characterized, which suggested its involvement in spermatogenesis. However, in this study, characterization of another Z-chromosome linked ubiquitin ligase Cs-rchy1 suggested it might function both in spermatogenesis and oogenesis, as well as the potential role in growth. These data may provide the genetic resource for gene editing or marker exploration in future. Abstract Ubiquitin ligase (E3) plays a versatile role in gonadal development and spermatogenesis in mammals, while its function in fish is little reported. In this study, a Z-chromosome linked ubiquitin ligase rchy1 in C. semilaevis (Cs-rchy1) was cloned and characterized. The full-length cDNA was composed of 1962 bp, including 551 bp 5′UTR, 736 bp 3′UTR, and 675 bp ORF encoding a 224-amino-acid (aa) protein. Cs-rchy1 was examined among seven different tissues and found to be predominantly expressed in gonads. In testis, Cs-rchy1 could be detected from 40 days post hatching (dph) until 3 years post hatching (yph), but there was a significant increase at 6 months post hatching (mph). In comparison, the expression levels in ovary were rather stable among different developmental stages. In situ hybridization showed that Cs-rchy1 was mainly localized in germ cells, that is, spermatid and spermatozoa in testis and stage I, II and III oocytes in ovary. In vitro RNA interference found that Cs-rchy1 knockdown resulted in the decline of sox9 and igf1 in ovarian cell line and down-regulation of cyp19a in the testicular cell line. These data suggested that Cs-rchy1 might participate in gonadal differentiation and gametogenesis, via regulating steroid hormone synthesis.
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Affiliation(s)
- Yuxuan Sun
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; (Y.S.); (Y.Z.); (P.C.); (M.Z.); (N.W.); (Z.C.)
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China;
| | - Ying Zhu
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; (Y.S.); (Y.Z.); (P.C.); (M.Z.); (N.W.); (Z.C.)
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266237, China
| | - Peng Cheng
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; (Y.S.); (Y.Z.); (P.C.); (M.Z.); (N.W.); (Z.C.)
| | - Mengqian Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; (Y.S.); (Y.Z.); (P.C.); (M.Z.); (N.W.); (Z.C.)
| | - Na Wang
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; (Y.S.); (Y.Z.); (P.C.); (M.Z.); (N.W.); (Z.C.)
| | - Zhongkai Cui
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; (Y.S.); (Y.Z.); (P.C.); (M.Z.); (N.W.); (Z.C.)
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China;
| | - Min Wei
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China;
| | - Wenteng Xu
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; (Y.S.); (Y.Z.); (P.C.); (M.Z.); (N.W.); (Z.C.)
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China;
- Correspondence: ; Tel./Fax: +86-(0)532-85831605
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Lobaton J, Andrew R, Duitama J, Kirkland L, Macfadyen S, Rader R. Using RNA-seq to characterize pollen-stigma interactions for pollination studies. Sci Rep 2021; 11:6635. [PMID: 33758263 PMCID: PMC7988043 DOI: 10.1038/s41598-021-85887-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
Insects are essential for the reproduction of pollinator-dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world’s food crops. Understanding pollen flow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the field is complex and laborious. We developed a field experiment in a pollinator-dependent crop and used high throughput RNA sequencing (RNA-seq) to quantify pollen flow by measuring changes in gene expression between pollination treatments across different apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with field data by observing single and multiple visits by honey bees (Apis mellifera) to apple flowers and measured fruit set in a commercial apple orchard. The first indicator of successful outcrossing was revealed via differential gene expression in the cross-pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specific genes related to pollen tube formation and defense response at three different time intervals in the stigma and the style following cross-pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specific to donor pollen could be detected in cross-pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or five flower visits by honey bees were insufficient and at least 10 honey bee flower visits were required to achieve a 25% probability of fruit set under orchard conditions. By combining the genotyping data, the differential expression analysis, and the traditional fruit set field experiments, it was possible to evaluate the pollination effectiveness of honey bee visits under orchards conditions. This is the first time that pollen-stigma-style mRNA expression analysis has been conducted after a pollinator visit (honey bee) to a plant (in vivo apple flowers). This study provides evidence that mRNA sequencing can be used to address complex questions related to stigma–pollen interactions over time in pollination ecology.
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Affiliation(s)
- Juan Lobaton
- School of Environmental and Rural Science, University of New England, Armidale, Australia. .,CSIRO, Clunies Ross St., Acton, ACT, Australia.
| | - Rose Andrew
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Jorge Duitama
- Systems and Computing, Engineering Department, Universidad de Los Andes, Bogota, Colombia
| | - Lindsey Kirkland
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | | | - Romina Rader
- School of Environmental and Rural Science, University of New England, Armidale, Australia
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McNinch C, Chen K, Dennison T, Lopez M, Yandeau-Nelson MD, Lauter N. A multigenotype maize silk expression atlas reveals how exposure-related stresses are mitigated following emergence from husk leaves. THE PLANT GENOME 2020; 13:e20040. [PMID: 33090730 DOI: 10.1002/tpg2.20040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/11/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
The extraordinarily long stigmatic silks of corn (Zea mays L.) are critical for grain production but the biology of their growth and emergence from husk leaves has remained underexplored. Accordingly, gene expression was assayed for inbreds 'B73' and 'Mo17' across five contiguous silk sections. Half of the maize genes (∼20,000) are expressed in silks, mostly in spatiotemporally dynamic patterns. In particular, emergence triggers strong differential expression of ∼1,500 genes collectively enriched for gene ontology terms associated with abiotic and biotic stress responses, hormone signaling, cell-cell communication, and defense metabolism. Further, a meta-analysis of published maize transcriptomic studies on seedling stress showed that silk emergence elicits an upregulated transcriptomic response that overlaps strongly with both abiotic and biotic stress responses. Although the two inbreds revealed similar silk transcriptomic programs overall, genotypic expression differences were observed for 5,643 B73-Mo17 syntenic gene pairs and collectively account for >50% of genome-wide expression variance. Coexpression clusters, including many based on genotypic divergence, were identified and interrogated via ontology-term enrichment analyses to generate biological hypotheses for future research. Ultimately, dissecting how gene expression changes along the length of silks and between husk-encased and emerged states offers testable models for silk development and plant response to environmental stresses.
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Affiliation(s)
- Colton McNinch
- Molecular, Cellular, and Developmental Biology Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
| | - Keting Chen
- Bioinformatics & Computational Biology Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
| | - Tesia Dennison
- Genetics & Genomics Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
| | - Miriam Lopez
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State Univ., Ames, IA, 50011, USA
| | - Marna D Yandeau-Nelson
- Molecular, Cellular, and Developmental Biology Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
- Bioinformatics & Computational Biology Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
- Genetics & Genomics Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
- Department of Genetics, Development and Cell Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Nick Lauter
- Molecular, Cellular, and Developmental Biology Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
- Genetics & Genomics Graduate Program, Iowa State Univ., Ames, IA, 50011, USA
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State Univ., Ames, IA, 50011, USA
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Zhang MJ, Zhang XS, Gao XQ. ROS in the Male-Female Interactions During Pollination: Function and Regulation. FRONTIERS IN PLANT SCIENCE 2020; 11:177. [PMID: 32180782 PMCID: PMC7059789 DOI: 10.3389/fpls.2020.00177] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/05/2020] [Indexed: 05/18/2023]
Abstract
The male-female interactions in pollination mediate pollen hydration and germination, pollen tube growth and fertilization. Reactive oxygen species (ROS) derived from both male and female tissues play regulatory roles for the communication between the pollen/pollen tube and female tissues at various stages, such as pollen hydration and germination on the stigma, pollen tube growth in the pistil and pollen tube reception in the female gametophyte. In this minireview, we primarily summarize the recent progress on the roles of ROS signaling in male-female interactions during pollination and discuss several ROS-regulated downstream signaling pathways for these interactions. Furthermore, several ROS-involved downstream pathways are outlined, such as Ca2+ signaling, cell wall cytomechanics, the redox modification of CRP, and cell PCD. At the end, we address the roles of ROS in pollen tube guidance and fertilization as future questions that merit study.
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Transcriptome Analysis Provides Insight into the Molecular Mechanisms Underlying gametophyte factor 2-Mediated Cross-Incompatibility in Maize. Int J Mol Sci 2018; 19:ijms19061757. [PMID: 29899298 PMCID: PMC6032218 DOI: 10.3390/ijms19061757] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/12/2018] [Accepted: 05/28/2018] [Indexed: 12/26/2022] Open
Abstract
In maize (Zea mays L.), unilateral cross-incompatibility (UCI) is controlled by Gametophyte factors (Ga), including Ga1, Ga2, and Tcb1; however, the molecular mechanisms underpinning this process remain unexplored. Here, we report the pollination phenotype of an inbred line, 511L, which carries a near-dominant Ga2-S allele. We performed a high-throughput RNA sequencing (RNA-Seq) analysis of the compatible and incompatible crosses between 511L and B73, to identify the transcriptomic differences associated with Ga2-mediated UCI. An in vivo kinetics analysis revealed that the growth of non-self pollen tubes was blocked at the early stages after pollination in 511L, maintaining the UCI barrier in Ga2. In total, 25,759 genes were expressed, of which, 2063 differentially expressed genes (DEGs) were induced by pollination (G_GG, G_GB, B_BB, B_BG). A gene ontology (GO) enrichment analysis revealed that these genes were specifically enriched in functions involved in cell wall strength and pectic product modification. Moreover, 1839, 4382, and 5041 genes were detected to differentially express under same pollination treatments, including B_G, BG_GG, and BB_GB, respectively. A total of 1467 DEGs were constitutively expressed between the two inbred lines following pollination treatments, which were enriched in metabolic processes, flavonoid biosynthesis, cysteine biosynthesis, and vacuole functions. Furthermore, we confirmed 14 DEGs related to cell wall modification and stress by qRT-PCR, which might be involved in Ga2-S-mediated UCI. Our results provide a comprehensive foundation for the molecular mechanisms involved in silks of UCI mediated by Ga2-S.
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Rutley N, Twell D. A decade of pollen transcriptomics. PLANT REPRODUCTION 2015; 28:73-89. [PMID: 25761645 PMCID: PMC4432081 DOI: 10.1007/s00497-015-0261-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/24/2015] [Indexed: 05/19/2023]
Abstract
Overview of pollen transcriptome studies. Pollen development is driven by gene expression, and knowledge of the molecular events underlying this process has undergone a quantum leap in the last decade through studies of the transcriptome. Here, we outline historical evidence for male haploid gene expression and review the wealth of pollen transcriptome data now available. Knowledge of the transcriptional capacity of pollen has progressed from genetic studies to the direct analysis of RNA and from gene-by-gene studies to analyses on a genomic scale. Microarray and/or RNA-seq data can now be accessed for all phases and cell types of developing pollen encompassing 10 different angiosperms. These growing resources have accelerated research and will undoubtedly inspire new directions and the application of system-based research into the mechanisms that govern the development, function and evolution of angiosperm pollen.
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Affiliation(s)
- Nicholas Rutley
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
| | - David Twell
- Department of Biology, University of Leicester, Leicester, LE1 7RH UK
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Nazemof N, Couroux P, Rampitsch C, Xing T, Robert LS. Proteomic profiling reveals insights into Triticeae stigma development and function. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6069-80. [PMID: 25170101 PMCID: PMC4203142 DOI: 10.1093/jxb/eru350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen-stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function.
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Affiliation(s)
- Nazila Nazemof
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON, Canada K1A 0C6 Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Philippe Couroux
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON, Canada K1A 0C6
| | - Christof Rampitsch
- Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB, Canada R6M 1Y5
| | - Tim Xing
- Carleton University, Department of Biology, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Laurian S Robert
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON, Canada K1A 0C6
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Yue X, Gao XQ, Wang F, Dong Y, Li X, Zhang XS. Transcriptional evidence for inferred pattern of pollen tube-stigma metabolic coupling during pollination. PLoS One 2014; 9:e107046. [PMID: 25215523 PMCID: PMC4162560 DOI: 10.1371/journal.pone.0107046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/07/2014] [Indexed: 01/08/2023] Open
Abstract
It is difficult to derive all qualitative proteomic and metabolomic experimental data in male (pollen tube) and female (pistil) reproductive tissues during pollination because of the limited sensitivity of current technology. In this study, genome-scale enzyme correlation network models for plants (Arabidopsis/maize) were constructed by analyzing the enzymes and metabolic routes from a global perspective. Then, we developed a data-driven computational pipeline using the "guilt by association" principle to analyze the transcriptional coexpression profiles of enzymatic genes in the consecutive steps for metabolic routes in the fast-growing pollen tube and stigma during pollination. The analysis identified an inferred pattern of pollen tube-stigma ethanol coupling. When the pollen tube elongates in the transmitting tissue (TT) of the pistil, this elongation triggers the mobilization of energy from glycolysis in the TT cells of the pistil. Energy-rich metabolites (ethanol) are secreted that can be taken up by the pollen tube, where these metabolites are incorporated into the pollen tube's tricarboxylic acid (TCA) cycle, which leads to enhanced ATP production for facilitating pollen tube growth. In addition, our analysis also provided evidence for the cooperation of kaempferol, dTDP-alpha-L-rhamnose and cell-wall-related proteins; phosphatidic-acid-mediated Ca2+ oscillations and cytoskeleton; and glutamate degradation IV for γ-aminobutyric acid (GABA) signaling activation in Arabidopsis and maize stigmas to provide the signals and materials required for pollen tube tip growth. In particular, the "guilt by association" computational pipeline and the genome-scale enzyme correlation network models (GECN) developed in this study was initiated with experimental "omics" data, followed by data analysis and data integration to determine correlations, and could provide a new platform to assist inachieving a deeper understanding of the co-regulation and inter-regulation model in plant research.
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Affiliation(s)
- Xun Yue
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
- College of Information Sciences and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Xin-Qi Gao
- College of Information Sciences and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Fang Wang
- College of Information Sciences and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - YuXiu Dong
- College of Information Sciences and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - XingGuo Li
- College of Information Sciences and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Xian Sheng Zhang
- College of Information Sciences and Engineering, Shandong Agricultural University, Taian, Shandong, China
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Moyle LC, Jewell CP, Kostyun JL. Fertile approaches to dissecting mechanisms of premating and postmating prezygotic reproductive isolation. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:16-23. [PMID: 24457825 DOI: 10.1016/j.pbi.2013.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/13/2013] [Accepted: 12/20/2013] [Indexed: 05/11/2023]
Abstract
In sexually reproducing organisms, speciation involves the evolution of mechanisms that confer reproductive isolation between diverging lineages. Here we discuss recent research on the molecular basis of traits that mediate these barriers during premating and postmating, prezygotic stages of reproduction. In some cases, the specific loci underlying the expression of reproductive barriers are known, most notably when premating isolation is due to flower color or scent differences, and when postmating isolation is due to divergent gamete signaling. In addition, emerging work in molecular biology and genomics is revealing the mechanistic basis of prezygotic reproductive traits within species, and therefore establishing clear candidates for future work examining their potential role in reproductive isolation between species.
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Affiliation(s)
- Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Cathleen P Jewell
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jamie L Kostyun
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Wang SS, Wang F, Tan SJ, Wang MX, Sui N, Zhang XS. Transcript profiles of maize embryo sacs and preliminary identification of genes involved in the embryo sac-pollen tube interaction. FRONTIERS IN PLANT SCIENCE 2014; 5:702. [PMID: 25566277 PMCID: PMC4269116 DOI: 10.3389/fpls.2014.00702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/25/2014] [Indexed: 05/05/2023]
Abstract
The embryo sac, the female gametophyte of flowering plants, plays important roles in the pollination and fertilization process. Maize (Zea mays L.) is a model monocot, but little is known about the interactions between its embryo sac and the pollen tube. In this study, we compared the transcript profiles of mature embryo sacs, mature embryo sacs 14-16 h after pollination, and mature nucelli. Comparing the transcript profiles of the embryo sacs before and after the entry of the pollen tube, we identified 3467 differentially expressed transcripts (3382 differentially expressed genes; DEGs). The DEGs were grouped into 22 functional categories. Among the DEGs, 221 genes were induced upon the entry of the pollen tube, and many of them encoded proteins involved in RNA binding, processing, and transcription, signaling, miscellaneous enzyme family processes, and lipid metabolism processes. Genes in the DEG dataset were grouped into 17 classes in a gene ontology enrichment analysis. The DEGs included many genes encoding proteins involved in protein amino acid phosphorylation and protein ubiquitination, implying that these processes might play important roles in the embryo sac-pollen tube interaction. Additionally, our analyses indicate that the expression of 112 genes encoding cysteine-rich proteins (CRPs) is induced during pollination and fertilization. The CRPs likely regulate pollen tube guidance and embryo sac development. These results provide important information on the genes involved in the embryo sac-pollen tube interaction in maize.
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Affiliation(s)
- Shuai Shuai Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural UniversityTai'an, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
| | - Su Jian Tan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
| | - Ming Xiu Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
| | - Na Sui
- College of Life Sciences, Shandong Normal UniversityJi'nan, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural UniversityTai'an, China
- *Correspondence: Xian Sheng Zhang, State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong Province, 271018 Shandong, China e-mail:
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Chung WH, Jeong N, Kim J, Lee WK, Lee YG, Lee SH, Yoon W, Kim JH, Choi IY, Choi HK, Moon JK, Kim N, Jeong SC. Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes. DNA Res 2013; 21:153-67. [PMID: 24271940 PMCID: PMC3989487 DOI: 10.1093/dnares/dst047] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/16/2013] [Indexed: 11/13/2022] Open
Abstract
Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions.
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Affiliation(s)
- Won-Hyong Chung
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Namhee Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Chungbuk 363-883, Republic of Korea
| | - Jiwoong Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Woo Kyu Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Chungbuk 363-883, Republic of Korea
| | - Yun-Gyeong Lee
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon 305-806, Republic of Korea
| | - Sang-Heon Lee
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon 305-806, Republic of Korea
| | - Woongchang Yoon
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Jin-Hyun Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
- Department of Genetic Engineering, Dong-A University, Busan 604-714, Republic of Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul 151-921, Republic of Korea
| | - Hong-Kyu Choi
- Department of Genetic Engineering, Dong-A University, Busan 604-714, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Namshin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon 305-806, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Chungbuk 363-883, Republic of Korea
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